8R9A

A soakable crystal form of human CDK7 in complex with AMP-PNP


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP277.2M Na2HPO4 20% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.3748.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 144.433α = 90
b = 40.417β = 90
c = 68.676γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2019-11-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA0.99987SLSX06DA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim I (All)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.7172.2285.50.1737.86.318453
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.711.7171.232

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT1.7172.221845399543.880.22360.21980.2939RANDOM35.144
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]
0.19-1.160.98
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.812
r_dihedral_angle_4_deg19.264
r_dihedral_angle_3_deg16.272
r_dihedral_angle_1_deg8.99
r_angle_refined_deg1.305
r_angle_other_deg0.457
r_chiral_restr0.063
r_bond_refined_d0.01
r_bond_other_d0.001
r_gen_planes_refined0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.812
r_dihedral_angle_4_deg19.264
r_dihedral_angle_3_deg16.272
r_dihedral_angle_1_deg8.99
r_angle_refined_deg1.305
r_angle_other_deg0.457
r_chiral_restr0.063
r_bond_refined_d0.01
r_bond_other_d0.001
r_gen_planes_refined0.001
r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2273
Nucleic Acid Atoms
Solvent Atoms207
Heterogen Atoms76

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
REFMACphasing