CHESS 7b2 Mac1 DNA beamtime
Last updated Mar 11, 2026 00:00

date: created: 2026-03-11 tags: - CHESS 7b2 - Mac1 - DNA

2026-03-11 @ CHESS 7b2

Third CHESS beam time of the 2026-1 run cycle.

Goals

  • Continue screening mac1 C2 crystals
  • Characterize new diode for flux measurement
  • Collect data from DNA crystals with 3' phosphate, +/- chemical ligation

Participants

Steve, Katie, & Xiaokun (Ando lab), with support from John I & Tricia C (CHESS)

  • katie_steve_xiaokun
    The DiffUSE team at CHESS beamline id7b2. From left to right: Katie, Steve, & Xiaokun.

  • katie_microscope
    Katie inspecting a mac1 crystal at CHESS.

Data

Root directory at CHESS: /nfs/chess/raw/2026-1/id7b2/meisburger/20260311

Root directory on OSN: s3://diffuse-chess-public/20260311

Beamline setup

parameter value notes
X-ray energy 14 keV @ 0.01% bandwidth Si 111 channel cut mono inserted
Beam size 100 µm x 100 µm Slit-defined, no CRL.
Flux 3.96 x 10^10 ph/s see CHESS nb #3 p. 84
Background reduction On-axis mirror with Mo tube only (no aperture)
Centering camera top-view and on-axis cameras Top view: 1.713 µm / pixel at 4x zoom ratio; On axis: 0.740 µm / pixel at 4x zoom ratio
Beamstop 700 µm diameter Mo disk suspended on mylar sheet, semi-transparent At this energy, the bleedthrough produces faint diffraction rings.
Data collection software "MX Collect" (python) & SPEC No changes since last time
Temperature control none
  • diode_front
    Si PIN diode (from James Holton, ALS) mounted on a magnetic base. The image is taken from the "front" side of the diode (X-ray beam was incident on this side).

  • diode_back
    The image is taken from the back side of the diode, which has a gold-colored contact.

Samples

Samples for single-crystal data collection were grown in 24-well hanging-drop vapor diffusion trays:

Name Sample Well composition Drop composition Notes
Mac1 (P43 space group) SARS CoV2 NSP3 macrodomain and seed stock from UCSF. 40 mg/mL Mac1 in 150 mM NaCl, 20 mM Tris pH 8, 5% glycerol 30% (w/vol) PEG 3000 + 100 mM CHES (pH 9.5) 2 µL protein + 1 µL well solution + 1 µL seeds (undiluted) Mac1 tray #3 (11/13/2025). See Katie L Ando Lab notebook p. 20
Mac1 (C2 space group) SARS CoV2 NSP3 macrodomain "C2" construct expressed and purified at Cornell. 15 mg/mL Mac1 in 150 mM NaCl, 20 mM Tris pH 8, 5% glycerol, 2 mM DTT 26-28% (w/vol) PEG 4000, 100 mM Tris (pH 8.3-8.8), 100 mM Na acetate 2 µL protein + 2 µL well solution (tray dated 3/5/26) or 2 µL protein + 1 µL well solution + 1 µL seeds (tray dated 1/27/26) Mac1 C2 trays dated 1/27/2026 and 3/5/2025. See Katie L Ando Lab notebook pp. 25, 26, 39
DNA S2T7-1, S2T7-2, and S2T7-3 single stranded oligos with 3'-phosphates at 50 µM in 40 mM tris acetate, 2 mM EDTA 125 mM tris acetate, 1.75 M ammonium sulfate, and 375 mM Mg acetate ("condition 1") or 37.5 mM Mg acetate (condition "2") 2.25 µL DNA + 0.75 µL well solution (3:1 ratio) DNA tray #3: S2T7-3'p (3/4/2026). See Steve's Ando Lab notebook #3, pp. 58, 59, 61-63, 65.
  • mac1_A4
    Mac1 crystals from well A4 of Katie's tray dated 11/13/2025. Well solution: 30% PEG 3000, 100 mM CHES pH 9.5. Drop: 2 µL protein + 1 µL well solution + 1 µL seeds

  • mac1_C2_A5
    Mac1 crystals from well A5 of Katie's C2 tray dated 1/27/2026. Well solution: 28% (w/vol) PEG 4000, 100 mM Tris (pH 8.3), 100 mM Na acetate. Drop: 2 µL protein + 1 µL well solution + 1 µL seeds

  • mac1_C2_C6
    Mac1 crystals from well C6 of Katie's C2 tray dated 1/27/2026. Well solution: 28% (w/vol) PEG 4000, 100 mM Tris (pH 8.3), 100 mM Na acetate. Drop: 2 µL protein + 1 µL well solution + 1 µL seeds (diluted 100-fold)

  • mac1_C2_B2
    Mac1 crystals from well B2 of Katie's C2 tray dated 3/5/2026. Well solution: 26% (w/vol) PEG 4000, 100 mM Tris (pH 8.8), 100 mM Na acetate. Drop: 2 µL protein + 2 µL well solution

  • DNA_A3
    DNA S2T7 (3' phosphate) crystals from well A3 of Steve's DNA tray #3 (3/4/2026). Well solution: 40 mM tris acetate, 375 mM Mg acetate, 1.75 M ammonium sulfate. Drop: 2.25 µL DNA + 0.75 µL well solution (3:1 ratio).

  • DNA_A6
    DNA S2T7 (3' phosphate) crystals from well A6 of Steve's DNA tray #3 (3/4/2026). Well solution: 40 mM tris acetate, 37.5 mM Mg acetate, 1.75 M ammonium sulfate. Drop: 2.25 µL DNA + 0.75 µL well solution (3:1 ratio).

  • DNA_A6_EDC
    DNA S2T7 (3' phosphate) crystals from well A6 of Steve's DNA tray #3 (3/4/2026) after washing and reacting with EDC for 12 h (3/9/2026). Wash solution: 40 mM MES pH 6.1, 37.5 mM MgCl2. Crosslinking solution: wash solution with 35 mg/mL EDC

Data collection

Steve arrived at 9:30 am with samples. Steve attached the diode to a magnetic base, and soldered on a BNC connector. John and Tricia aligned the optics, handed off to Steve at noon.

All crystal handling was done in the humidity-controlled chamber (100% RH) unless noted. Crystals were mounted using reusable magnetic bases and micro-RT sleeves, cut to length (~18 mm), with 10 µL reservoir solution in the tip.

Note that the flux is down a factor of ~2 since last time. This is probably down to changes in the focus of the toroidal mirror. Will increase exposure times to compensate.

1. Mac1 (P43)

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Katie looped a ~300 µm mac1 crystal (P43 space group) from well A4 of the tray dated 11/13/2025.

Subdirectory: mac1/mac1_1

Recorded 12 images: mac1_1_oac_zoom2_*.png

prefix φ0 (deg.) φ1 (deg.) ∆φ (deg.) images ∆t (s) tf (%) d (mm) E (keV)
mac1_1_3012 0 360 0.1 3600 0.02 100 185 14
mac1_1_bg_3013 0 360 1 360 0.2 100 185 14

Note: dials failed to index beyond frame ~1800. The loop is slightly oversized, and it's likely the crystal slipped during data collection.

??? info "xia2 processing"

Re-ran xia2 on the first 1800 frames only.

|                 | mac1_1_3012                           |
|-----------------|---------------------------------------|
| Mosaic spread   | 0.012                                 |
| Resolution      | 1.04                                  |
| Unit Cell       | [89.0, 89.0, 40.14, 90.0, 90.0, 90.0] |
| Image range     | [1, 1800]                             |
| Completeness    | 87.7                                  |
| Multiplicity    | 5.6                                   |
| I/sigma         | 6.6                                   |
| Rpim            | 0.062                                 |
| Wilson B factor | 12.4                                  |
| Space group     | P 43                                  |

2. Mac1 (C2)

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Xiaokun looped a chunky mac1 crystal (C2 space group) from well A5 of tray dated 1/27/2026 using an EV loop (70 x 700 µm). There is a large amount of PEG skin / precipitate coating the crystal.

Subdirectory: mac1_c2/mac1_c2_1

Recorded 12 images: mac1_c2_1_oac_zoom1_*.png

Vector scan.

prefix φ0 (deg.) φ1 (deg.) ∆φ (deg.) images ∆t (s) tf (%) d (mm) E (keV)
mac1_c2_1_3014 0 720 0.1 7200 0.02 100 500 14
mac1_c2_1_3015 0 720 0.1 7200 0.02 100 185 14
mac1_c2_1_3016 0 720 0.1 7200 0.02 100 185 14

!!! warning

- scan `3014` (first dataset) -- I accidentally started collection with the detector at 500 mm. I quickly closed the shutter to prevent damage.
- scan `3015` (second dataset) -- I forgot to open the shutter again (duh!).
- The start of data collection looks OK, but bad spots / multiple lattice appear quickly after.
- Didn't bother with a background.

I ran xia2 on the first 1800 images. The unit cell is really interesting, we're getting a beta angle of 98˚, while before it was 103˚. The PDB has examples of both for this space group (for example, 7KR0 vs. 7KR1). Since this is an old tray, it's possible this crystal nucleated much later, and represents a dehydrated form.

!!! note "About C2 isoforms"

The [Science Advances paper](https://doi.org/10.1126/sciadv.abf8711) describes three C2 isoforms that appeared during fragment screening (Figure S2 in the [Supplementary Material](https://www.science.org/doi/suppl/10.1126/sciadv.abf8711/suppl_file/abf8711_sm.pdf)). They are distinguished by the a and c axis lengths:

| isoform label | a | c | example PDB entry | beta angle (from PDB entry)
| --- | --- | --- | --- | ---
| A   | 130 | 39.5 | [7KQW](https://www.rcsb.org/structure/7KQW) | 96.69
| B   | 133 | 37.5 | [7KR1](https://www.rcsb.org/structure/7KR1) | 98.95
| C   | 138 | 38.0 | [7KR0](https://www.rcsb.org/structure/7KR0) | 103.56

??? info "xia2 processing"

Processed first and second halves of the dataset separately.

|                 | mac1_c2_1_3016                           | mac1_c2_1_3016                           |
|-----------------|------------------------------------------|------------------------------------------|
| Mosaic spread   | 0.237                                    | 0.294                                    |
| Resolution      | 1.63                                     | 1.32                                     |
| Unit Cell       | [134.57, 30.39, 37.8, 90.0, 98.85, 90.0] | [134.65, 30.39, 37.8, 90.0, 98.67, 90.0] |
| Image range     | [1800, 3600]                             | [1, 1800]                                |
| Completeness    | 99.9                                     | 99.0                                     |
| Multiplicity    | 3.3                                      | 3.3                                      |
| I/sigma         | 21.6                                     | 9.4                                      |
| Rpim            | 0.057                                    | 0.05                                     |
| Wilson B factor | 19.55                                    | 15.78                                    |
| Space group     | C 1 2 1                                  | C 1 2 1                                  |

3. Mac1 (C2)

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Xiaokun looped a small needle from well B2 of the tray dated 3/5/2026.

Subdirectory: mac1_c2/mac1_c2_2

Recorded 12 images: mac1_c2_2_oac_zoom4_*.png

prefix φ0 (deg.) φ1 (deg.) ∆φ (deg.) images ∆t (s) tf (%) d (mm) E (keV)
mac1_c2_2_3017 0 360 0.1 3600 0.01 100 185 14
mac1_c2_2_bg_3018 0 360 1 360 0.1 100 185 14

??? info "xia2 processing"

Noticed that the first 90 degrees has a very high Rmerge, so I removed these frames and re-ran xia2.

|                 | mac1_c2_2_3017                            | mac1_c2_2_3017                             |
|-----------------|-------------------------------------------|--------------------------------------------|
| Mosaic spread   | 0.164                                     | 0.037                                      |
| Resolution      | 1.37                                      | 1.27                                       |
| Unit Cell       | [139.7, 30.19, 38.22, 90.0, 103.07, 90.0] | [139.71, 30.19, 38.22, 90.0, 103.07, 90.0] |
| Image range     | [1, 3600]                                 | [901, 3600]                                |
| Completeness    | 98.3                                      | 97.8                                       |
| Multiplicity    | 6.9                                       | 5.1                                        |
| I/sigma         | 10.5                                      | 10.1                                       |
| Rpim            | 0.061                                     | 0.047                                      |
| Wilson B factor | 16.41                                     | 14.3                                       |
| Space group     | C 1 2 1                                   | C 1 2 1                                    |

4. Mac1 (C2)

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Xiaokun looped another thin crystal from well B2 of the tray dated 3/5/2026. This one is really really thin!

Beam size reduced to 30 x 30 µm.

Vector scan.

Subdirectory: mac1_c2/mac1_c2_3

Recorded 12 crystal images: mac1_c2_3_oac_zoom4_*.png

prefix φ0 (deg.) φ1 (deg.) ∆φ (deg.) images ∆t (s) tf (%) d (mm) E (keV)
../mac1_c2_2/mac1_c2_2_bg_3019 0 360 0.1 3600 0.04 100 185 14
mac1_c2_3_bg_3020 0 360 1 360 0.4 100 185 14

!!! warning "file naming error"

I accidentally collected the dataset in the `mac1_c2_2` subdirectory with prefix `mac1_c2_2_bg`. It should have been `mac1_c2_3/mac1_c2_3`.

??? info "xia2 processing"

|                 | mac1_c2_2_bg_3019                          |
|-----------------|--------------------------------------------|
| Mosaic spread   | 0.121                                      |
| Resolution      | 1.73                                       |
| Unit Cell       | [139.49, 30.15, 38.17, 90.0, 102.98, 90.0] |
| Image range     | [1001, 3600]                               |
| Completeness    | 98.9                                       |
| Multiplicity    | 5.0                                        |
| I/sigma         | 3.5                                        |
| Rpim            | 0.137                                      |
| Wilson B factor | 17.81                                      |
| Space group     | C 1 2 1                                    |

5. Mac1 (C2)

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Xiaokun looped another mac1 crystal from well B2 of the tray dated 3/5/2026. This one is much chunkier, and hangs off the end of the loop.

Beam size increased to 50 x 50 µm.

Subdirectory: mac1_c2/mac1_c2_4

Recorded 12 crystal images: mac1_c2_4_oac_zoom4_*.png

Vector scan.

prefix φ0 (deg.) φ1 (deg.) ∆φ (deg.) images ∆t (s) tf (%) d (mm) E (keV)
mac1_c2_4_3021 0 360 0.1 3600 0.04 100 185 14
mac1_c2_4_bg_3022 0 360 1 360 0.4 100 185 14

??? info "xia2 processing"

Reprocessed with frame range 1001:2000, because the ends did not index well.

|                 | mac1_c2_4_3021                            |
|-----------------|-------------------------------------------|
| Mosaic spread   | 0.408                                     |
| Resolution      | 1.62                                      |
| Unit Cell       | [139.34, 30.1, 38.14, 90.0, 102.96, 90.0] |
| Image range     | [1001, 2000]                              |
| Completeness    | 79.1                                      |
| Multiplicity    | 2.4                                       |
| I/sigma         | 8.9                                       |
| Rpim            | 0.068                                     |
| Wilson B factor | 17.41                                     |
| Space group     | C 1 2 1                                   |

Flux measurement

Steve placed the diode on the goniometer so that it was 'vertical' when phi = 0. The beamstop was removed, and a 6 cm N2 gas ion chamber (I2) was placed downstream. A small ion chamber (ICol) was upstream of the sample.

The ion chambers and diodes were connected to SRS current amplifiers with gain settings of 50 nA/V (I2) and 10 µA/V (Diode). The SPEC counter-timer board has a conversion of 10 V = 1 MHz (in other words, 100,000 counts per second = 1 V).

Subdirectory: diode/, SPEC file: diode_1.spec

In SPEC, ICol ion chamber was set monitor, and the diode current (Diode) was set to 'detector'. The ICol counter rate was ~150,000 per second.

First scan, with the beam going through the diode:

dscan phi -60 60 12 -150000

Second scan, the beam is off the tip of the diode:

dscan phi -60 60 12 -150000

Here's the result:

diode_current

Lets calculate flux assuming all absorbed photons are converted into charge carriers. The max transmission is 0.253, so fraction absorbed is 0.747. At 14 keV, the number of charge carriers generated per photon absorbed is 14,000 eV / 3.66 eV = 3825. Accounting for the absorbed fraction, the conversion would be 1 photon/sec ~ 4.578e-16 A (4.578e-10 µA). The observed current is 15.5 µA, so flux = 15.5/4.578e-10 = 3.38e10 ph/s.

The I2 counts recorded during the second scan (bypassing the diode) were 39756. According to the CHESS ion chamber flux calculator this is 3.38e10 ph/s. So both methods agree. The fact that they agree to 2 decimal praces is accidental; according to James H the diode response varies across the surface, setting an empirical error bar of something like 5%.

6. Mac1 (C2)

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Katie looped a big crystal from well C6 of mac1 C2 tray dated 1/27/2026 using a 700 µm EV loop.

Subdirectory: mac1_c2/mac1_c2_5

Recorded 12 crystal images: mac1_c2_5_oac_zoom1_*.png

Vector scan.

prefix φ0 (deg.) φ1 (deg.) ∆φ (deg.) images ∆t (s) tf (%) d (mm) E (keV)
mac1_c2_5_3023 0 720 0.1 7200 0.02 100 185 14
mac1_c2_5_bg_3024 0 720 1 720 0.2 100 185 14

!!! warning "poor diffraction"

Looks like multiple lattices. There are also diffraction rings from beamstop visible, probably some misalignment that needs to be corrected.

Steve left for dinner.


Steve and Xiaokun returned at 10:40 pm.

7. DNA

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Steve looped the first DNA crystal from well A3, of tray labeled "DNA 3' phos" using a 150 µm loop. This crystal is from "condition 1", which has high magnesium concentration.

Subdirectory: dna/dna_1

Recorded 12 crystal images: dna_1_oac_zoom4_*.png

prefix φ0 (deg.) φ1 (deg.) ∆φ (deg.) images ∆t (s) tf (%) d (mm) E (keV)
dna_1_3031 0 360 0.1 3600 0.01 47.2 185 14
dna_1_bg_3032 0 360 1 360 0.1 47.2 185 14
dna_1_3033 330 340 0.1 100 0.2 100 185 14

??? info "xia2 processing"

|                 | dna_1_3031                                 |
|-----------------|--------------------------------------------|
| Mosaic spread   | 0.043                                      |
| Resolution      | 4.9                                        |
| Unit Cell       | [107.98, 107.98, 92.01, 90.0, 90.0, 120.0] |
| Image range     | [1, 3600]                                  |
| Completeness    | 100.0                                      |
| Multiplicity    | 10.3                                       |
| I/sigma         | 9.2                                        |
| Rpim            | 0.02                                       |
| Wilson B factor | 322.68                                     |
| Space group     | R 3                                        |

8. DNA

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Steve looped a second DNA crystal from well A3 of the same tray.

Subdirectory: dna/dna_2

Recorded 12 images: dna_2_oac_zoom4_*.png

prefix φ0 (deg.) φ1 (deg.) ∆φ (deg.) images ∆t (s) tf (%) d (mm) E (keV)
dna_2_3034 0 360 0.1 3600 0.01 47.2 185 14
dna_2_bg_3035 0 360 1 360 0.1 47.2 185 14
dna_2_3036 60 70 0.1 100 0.2 100 185 14

??? info "xia2 processing"

|                 | dna_2_3034                                 |
|-----------------|--------------------------------------------|
| Mosaic spread   | 0.028                                      |
| Resolution      | 5.53                                       |
| Unit Cell       | [107.81, 107.81, 94.62, 90.0, 90.0, 120.0] |
| Image range     | [1, 3600]                                  |
| Completeness    | 100.0                                      |
| Multiplicity    | 10.2                                       |
| I/sigma         | 12.2                                       |
| Rpim            | 0.019                                      |
| Wilson B factor | 391.19                                     |
| Space group     | R 3                                        |

9. DNA + EDC

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Steve looped a cross-linked crystal, originally from well A6 of the "DNA 3' phos" tray. It was grown in "condition 2" (low magnesium concentration), washed with MgCl2 and MES buffer at pH 6.1, then cross-linked with 35 mg/mL EDC overnight.

Subdirectory: dna/dna_3

Recorded 12 images: dna_3_oac_zoom4_*.png

prefix φ0 (deg.) φ1 (deg.) ∆φ (deg.) images ∆t (s) tf (%) d (mm) E (keV)
dna_3_3037 0 360 0.1 3600 0.01 47.2 185 14
dna_3_bg_3038 0 360 1 360 0.1 47.2 185 14

This diffracts better than expected, given the appearance!

??? info "xia2 processing"

|                 | dna_3_3037                                 |
|-----------------|--------------------------------------------|
| Mosaic spread   | 0.101                                      |
| Resolution      | 4.9                                        |
| Unit Cell       | [108.99, 108.99, 94.55, 90.0, 90.0, 120.0] |
| Image range     | [1, 3600]                                  |
| Completeness    | 100.0                                      |
| Multiplicity    | 10.4                                       |
| I/sigma         | 11.4                                       |
| Rpim            | 0.014                                      |
| Wilson B factor | 299.43                                     |
| Space group     | R 3                                        |

There is no apparent radiation damage during this data collection, so repeat with 4x the dose.

prefix φ0 (deg.) φ1 (deg.) ∆φ (deg.) images ∆t (s) tf (%) d (mm) E (keV)
dna_3_3039 0 360 0.1 3600 0.02 100 185 14

??? info "xia2 processing"

|                 | dna_3_3039                                 |
|-----------------|--------------------------------------------|
| Mosaic spread   | 0.107                                      |
| Resolution      | 4.63                                       |
| Unit Cell       | [108.99, 108.99, 94.61, 90.0, 90.0, 120.0] |
| Image range     | [1, 3600]                                  |
| Completeness    | 100.0                                      |
| Multiplicity    | 10.5                                       |
| I/sigma         | 15.3                                       |
| Rpim            | 0.012                                      |
| Wilson B factor | 325.56                                     |
| Space group     | R 3                                        |

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The crystal was removed from the goniometer, and then placed in a drop of water under the microscope. Recorded a 3 minute video. Wow, it didn't dissolve!

Looped the crystal out of the drop (in air, not in the humidity chamber), and put the sleeve back on.

Oops, it looks dried out / opaque. Let's just take a snapshot.

Subdirectory: dna/dna_3_wat

(unfortunately, neglected to take a picture)

prefix φ0 (deg.) ∆φ (deg.) images ∆t (s) tf (%) d (mm) E (keV)
dna_3_wat_3040 330 0.5 1 1 100 185 14

Wow, what a weird diffraction pattern. Crystal is definitely not happy.

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Can we rehydrate it? Removed the crystal from the goniometer, and placed back in water droplet. Looped in the humidity chamber this time, and placed the sleeve on.

Subdirectory: dna/dna_3_wat2

Saved 12 images: dna_3_wat2_oac_zoom4_*.png

Let's take a 1 second snapshot

prefix φ0 (deg.) φ1 (deg.) ∆φ (deg.) images ∆t (s) tf (%) d (mm) E (keV)
dna_3_wat2_3041 15 nan 0.5 1 1 100 185 14

Amazing, diffraction recovered! Collect another dataset

prefix φ0 (deg.) φ1 (deg.) ∆φ (deg.) images ∆t (s) tf (%) d (mm) E (keV)
dna_3_wat2_3042 0 360 0.1 3600 0.01 47.2 185 14
dna_3_wat2_bg_3043 0 360 1 360 0.1 47.2 185 14

??? info "xia2 processing"

|                 | dna_3_wat2_3042                            |
|-----------------|--------------------------------------------|
| Mosaic spread   | 0.149                                      |
| Resolution      | 5.47                                       |
| Unit Cell       | [108.96, 108.96, 98.55, 90.0, 90.0, 120.0] |
| Image range     | [1, 3600]                                  |
| Completeness    | 100.0                                      |
| Multiplicity    | 10.1                                       |
| I/sigma         | 13.0                                       |
| Rpim            | 0.015                                      |
| Wilson B factor | 320.19                                     |
| Space group     | R 3                                        |

Here's what the diffraction patterns look like (referred to above):

  • dna_3_wat_diffraction
    Snapshot diffraction pattern from the dehydrated DNA + EDC crystal, dna_3_wat_3040.

  • dna_3_wat2_diffraction
    Snapshot diffraction pattern after rehydrating, dna_3_wat2_3041.

!!! success "Done!"