5AND

Crystal structure of CDK2 in complex with 2-imidazol-1-yl-1H- benzimidazole processed with the CrystalDirect automated mounting and cryo-cooling technology


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1HCLPDB ENTRY 1HCL

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
10.02 M HEPES, PH=7.0, 5% GLYCEROL, 12% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.0239.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.616α = 90
b = 70.568β = 90
c = 72.448γ = 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 ID29ESRFID29

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
12.329.4799.90.146.5127402

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1HCL2.329.471206762399.80.202310.200230.24295RANDOM52.283
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]
-0.02-0.090.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.744
r_dihedral_angle_3_deg15.341
r_dihedral_angle_4_deg14.156
r_dihedral_angle_1_deg5.942
r_mcangle_it5.781
r_scbond_it5.626
r_mcbond_other3.776
r_mcbond_it3.774
r_angle_refined_deg1.605
r_angle_other_deg0.856
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.744
r_dihedral_angle_3_deg15.341
r_dihedral_angle_4_deg14.156
r_dihedral_angle_1_deg5.942
r_mcangle_it5.781
r_scbond_it5.626
r_mcbond_other3.776
r_mcbond_it3.774
r_angle_refined_deg1.605
r_angle_other_deg0.856
r_chiral_restr0.086
r_bond_refined_d0.013
r_gen_planes_refined0.007
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 Atoms2194
Nucleic Acid Atoms
Solvent Atoms83
Heterogen Atoms14

Software

Software
Software NamePurpose
REFMACrefinement
MOLREPphasing