5IEV

Crystal structure of BAY 1000394 (Roniciclib) bound to CDK2


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.8293.157.25% PEG 4000, 0.2M ammonium acetate, 100mM Hepes pH 7.8
Crystal Properties
Matthews coefficientSolvent content
2.0740.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.776α = 90
b = 71.814β = 90
c = 72.901γ = 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
12.0343.2895.912.053.5917101

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 REPLACEMENTTHROUGHOUT2.0343.281710190195.50.198430.195150.2615RANDOM21.564
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]
-0.3-2.973.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.317
r_dihedral_angle_3_deg16.77
r_dihedral_angle_4_deg16.728
r_long_range_B_refined6.832
r_long_range_B_other6.805
r_dihedral_angle_1_deg6.17
r_scangle_other2.951
r_mcangle_it2.645
r_mcangle_other2.645
r_angle_refined_deg1.892
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.317
r_dihedral_angle_3_deg16.77
r_dihedral_angle_4_deg16.728
r_long_range_B_refined6.832
r_long_range_B_other6.805
r_dihedral_angle_1_deg6.17
r_scangle_other2.951
r_mcangle_it2.645
r_mcangle_other2.645
r_angle_refined_deg1.892
r_scbond_it1.835
r_scbond_other1.835
r_mcbond_it1.631
r_mcbond_other1.631
r_angle_other_deg0.911
r_chiral_restr0.106
r_bond_refined_d0.016
r_gen_planes_refined0.009
r_bond_other_d0.001
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 Atoms2309
Nucleic Acid Atoms
Solvent Atoms154
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing