8YSE
Crystal structure of the Deinococcus wulumuqiensis CD-NTase DwCdnB in complex with dATP
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 277 | 2 % v/v Tacsimate, 0.1 M Bis-Tris pH 6.5, 20 % w/v PEG 3350. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.31 | 46.82 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 35.355 | α = 99.56 |
b = 46.614 | β = 105.81 |
c = 59.644 | γ = 100.12 |
Symmetry | |
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Space Group | P 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | PIXEL | DECTRIS EIGER2 X 9M | 2021-05-11 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSRRC BEAMLINE TPS 05A | 0.99984 | NSRRC | TPS 05A |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Net I Over Average Sigma (I) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot | ||||||||
1 | 2.19 | 30 | 96.2 | 0.019 | 37.853 | 2.1 | 17231 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.19 | 2.28 | 95.5 | 0.995 | 2.2 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 2.19 | 22 | 16353 | 853 | 95.45 | 0.16521 | 0.16353 | 0.19571 | RANDOM | 34.384 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
0.23 | -0.03 | 0.1 | 0.06 | -0.54 | -0.02 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.849 |
r_dihedral_angle_4_deg | 18.348 |
r_dihedral_angle_3_deg | 15.681 |
r_long_range_B_other | 7.542 |
r_long_range_B_refined | 7.534 |
r_dihedral_angle_1_deg | 6.451 |
r_scangle_other | 5.926 |
r_mcangle_it | 4.64 |
r_mcangle_other | 4.639 |
r_scbond_it | 3.795 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2627 |
Nucleic Acid Atoms | |
Solvent Atoms | 147 |
Heterogen Atoms | 62 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
Blu-Ice | data collection |
HKL-2000 | data scaling |