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CDK2 in complex with AZD5438
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5MHQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 10MG/ML CDK2 10% V/V PEG3350, 50 MM HEPES/NAOH, 50 MM NA/K PHOSPHATE, PH 7.5
Crystal Properties Matthews coefficient Solvent content 1.97 37.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.321 α = 90 b = 71.296 β = 90 c = 72.114 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 2017-03-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.987 Diamond I04
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 1.5 50.75 100 0.05 13.5 6.9 44735
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.53 100 1.5 7.1
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 MOLECULAR REPLACEMENT THROUGHOUT 5MHQ 1.5 50.75 42508 2227 99.97 0.20119 0.19893 0.2065 0.2433 0.2506 RANDOM 33.24
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] 0.18 0.9 -1.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.864 r_dihedral_angle_4_deg 17.807 r_dihedral_angle_3_deg 15.817 r_long_range_B_refined 8.023 r_long_range_B_other 8.023 r_scangle_other 6.116 r_dihedral_angle_1_deg 6.08 r_mcangle_other 4.321 r_mcangle_it 4.318 r_scbond_it 4.095
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.864 r_dihedral_angle_4_deg 17.807 r_dihedral_angle_3_deg 15.817 r_long_range_B_refined 8.023 r_long_range_B_other 8.023 r_scangle_other 6.116 r_dihedral_angle_1_deg 6.08 r_mcangle_other 4.321 r_mcangle_it 4.318 r_scbond_it 4.095 r_scbond_other 4.095 r_angle_other_deg 3.573 r_mcbond_it 3.222 r_mcbond_other 3.213 r_angle_refined_deg 2.092 r_chiral_restr 0.138 r_bond_refined_d 0.021 r_gen_planes_other 0.018 r_gen_planes_refined 0.012 r_bond_other_d 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 Atoms Number Protein Atoms 2302 Nucleic Acid Atoms Solvent Atoms 156 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing