8BUH
Structure of DDB1 bound to WX3-engaged CDK12-cyclin K
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 6TD3 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | 0.7 M ammonium sulfate, 0.45 M ammonium citrate, 0.07 M HEPES pH 7 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.93 | 68.68 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 249.143 | α = 90 |
b = 249.143 | β = 90 |
c = 217.39 | γ = 120 |
Symmetry | |
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Space Group | P 31 2 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 16M | 2021-06-27 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X10SA | 1.0 | SLS | X10SA |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | CC (Half) | 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 | 3.789 | 215.765 | 95.5 | 0.994 | 7 | 21.2 | 63976 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 3.789 | 4.019 | 0.294 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 3.79 | 37.21 | 1.33 | 63861 | 3167 | 82.46 | 0.1888 | 0.1866 | 0.232 | 152.66 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 11.8041 |
f_angle_d | 0.8749 |
f_chiral_restr | 0.0535 |
f_plane_restr | 0.0061 |
f_bond_d | 0.0059 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 33494 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 159 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
XDS | data reduction |
Coot | model building |
STARANISO | data scaling |
autoPROC | data processing |
PHASER | phasing |