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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
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 0.02 M HEPES, PH=7.0, 5% GLYCEROL, 12% PEG 3350
Crystal Properties Matthews coefficient Solvent content 1.87 34.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.052 α = 90 b = 51.728 β = 90 c = 71.265 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.9 30 99.9 0.07 6.4 20768 2.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION OTHER THROUGHOUT NONE 1.9 30 19657 1064 99.88 0.19693 0.19488 0.2055 0.2359 0.244 RANDOM 48.579
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 Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.152 r_dihedral_angle_4_deg 19.477 r_dihedral_angle_3_deg 15.08 r_dihedral_angle_1_deg 6.325 r_scbond_it 5.89 r_mcangle_it 5.397 r_mcbond_other 3.95 r_mcbond_it 3.948 r_angle_refined_deg 1.826 r_angle_other_deg 0.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.152 r_dihedral_angle_4_deg 19.477 r_dihedral_angle_3_deg 15.08 r_dihedral_angle_1_deg 6.325 r_scbond_it 5.89 r_mcangle_it 5.397 r_mcbond_other 3.95 r_mcbond_it 3.948 r_angle_refined_deg 1.826 r_angle_other_deg 0.93 r_chiral_restr 0.106 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_bond_other_d 0.006 r_gen_planes_other 0.002 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 Atoms Number Protein Atoms 2204 Nucleic Acid Atoms Solvent Atoms 115 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement