5ANK

Crystal structure of CDK2 in complex with 2,4,6-trioxo-1-phenyl- hexahydropyrimidine-5-carboxamide processed with the CrystalDirect automated mounting and cryo-cooling technology


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
10.02 M HEPES, PH=7.0, 5% GLYCEROL, 12% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
1.8734.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.052α = 90
b = 51.728β = 90
c = 71.265γ = 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
1SYNCHROTRONESRF BEAMLINE ID23-1ESRFID23-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.93099.90.076.4207682.4

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 DIFFRACTIONOTHERTHROUGHOUTNONE1.93019657106499.880.196930.194880.2359RANDOM48.579
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]
3.51-1.53-1.98
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.152
r_dihedral_angle_4_deg19.477
r_dihedral_angle_3_deg15.08
r_dihedral_angle_1_deg6.325
r_scbond_it5.89
r_mcangle_it5.397
r_mcbond_other3.95
r_mcbond_it3.948
r_angle_refined_deg1.826
r_angle_other_deg0.93
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.152
r_dihedral_angle_4_deg19.477
r_dihedral_angle_3_deg15.08
r_dihedral_angle_1_deg6.325
r_scbond_it5.89
r_mcangle_it5.397
r_mcbond_other3.95
r_mcbond_it3.948
r_angle_refined_deg1.826
r_angle_other_deg0.93
r_chiral_restr0.106
r_bond_refined_d0.016
r_gen_planes_refined0.009
r_bond_other_d0.006
r_gen_planes_other0.002
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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2204
Nucleic Acid Atoms
Solvent Atoms115
Heterogen Atoms18

Software

Software
Software NamePurpose
REFMACrefinement