8YSO
Crystal structure of the Deinococcus wulumuqiensis CD-NTase DwCdnB Ear-cut mutant in complex with ATP
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 8YSN |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 277 | 0.1 M Bis-Tris pH 6.5, 0.2 M Sodium fluoride, 23 % w/v PEG 3350. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.31 | 46.83 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 49.331 | α = 90 |
b = 72.832 | β = 90 |
c = 100.998 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 16M | 2022-12-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSRRC BEAMLINE TPS 07A | 0.97625 | NSRRC | TPS 07A |
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 | 1.68 | 30 | 99.4 | 0.058 | 47.067 | 12 | 42038 |
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 | 1.68 | 1.74 | 0.917 |
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 (All) | R-Work | R-Free | Mean Isotropic B | ||||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 1.68 | 23.973 | 41873 | 2118 | 99.056 | 0.172 | 0.1709 | 0.1994 | 16.584 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[2][2] | Anisotropic B[3][3] | ||||
0.166 | 0.11 | -0.276 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 31.933 |
r_dihedral_angle_4_deg | 15.4 |
r_dihedral_angle_3_deg | 12.471 |
r_dihedral_angle_1_deg | 6.649 |
r_lrange_it | 5.826 |
r_lrange_other | 5.67 |
r_scangle_it | 4.305 |
r_scangle_other | 4.279 |
r_mcangle_it | 2.741 |
r_mcangle_other | 2.741 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2474 |
Nucleic Acid Atoms | |
Solvent Atoms | 315 |
Heterogen Atoms | 69 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
Blu-Ice | data collection |
HKL-2000 | data scaling |