7N3U

Crystal structure of human WEE1 kinase domain in complex with ZN-c3


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5V5Y 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8291.1520% PEG 20K
Crystal Properties
Matthews coefficientSolvent content
2.1642.94

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.92α = 90
b = 50.51β = 90
c = 119.58γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9M2020-03-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-D1.12723APS21-ID-D

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
12.6546.5799.80.0850.0890.0270.99817.510.28565
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.652.7899.70.7830.8220.2470.9310.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5V5Y2.6546.53809543099.650.21960.21690.2668RANDOM71.916
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]
-1.97-6.698.66
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.938
r_dihedral_angle_3_deg17.304
r_dihedral_angle_4_deg13.779
r_dihedral_angle_1_deg7.076
r_angle_refined_deg1.346
r_angle_other_deg1.126
r_chiral_restr0.049
r_bond_refined_d0.005
r_gen_planes_refined0.005
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.938
r_dihedral_angle_3_deg17.304
r_dihedral_angle_4_deg13.779
r_dihedral_angle_1_deg7.076
r_angle_refined_deg1.346
r_angle_other_deg1.126
r_chiral_restr0.049
r_bond_refined_d0.005
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2079
Nucleic Acid Atoms
Solvent Atoms29
Heterogen Atoms39

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing