5IEY

Crystal structure of a CDK inhibitor bound to CDK2


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.8293.157.25% PEG 4000, 0.2 M ammonium acetate, 0.2 M HEPES pH 7.8
Crystal Properties
Matthews coefficientSolvent content
2.0239.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.337α = 90
b = 71.983β = 90
c = 72.037γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.918BESSY14.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
11.6642.8797.810.694.2530887

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.6642.8730887162697.80.181920.179630.22502RANDOM39.682
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]
-0.862.08-1.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.785
r_dihedral_angle_4_deg17.196
r_dihedral_angle_3_deg14.899
r_long_range_B_refined7.665
r_long_range_B_other7.654
r_dihedral_angle_1_deg6.083
r_scangle_other4.621
r_scbond_it3.154
r_scbond_other3.153
r_mcangle_it3.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.785
r_dihedral_angle_4_deg17.196
r_dihedral_angle_3_deg14.899
r_long_range_B_refined7.665
r_long_range_B_other7.654
r_dihedral_angle_1_deg6.083
r_scangle_other4.621
r_scbond_it3.154
r_scbond_other3.153
r_mcangle_it3.15
r_mcangle_other3.149
r_mcbond_it2.298
r_mcbond_other2.298
r_angle_refined_deg1.949
r_angle_other_deg0.977
r_chiral_restr0.129
r_bond_refined_d0.018
r_gen_planes_refined0.011
r_bond_other_d0.002
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2296
Nucleic Acid Atoms
Solvent Atoms192
Heterogen Atoms23

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing