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Complex structure of CDK2/Cyclin E1 and a potent, selective small molecule inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1W98
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291.15 0.2 M sodium citrate pH 6.5, 10% PEG3350
Crystal Properties Matthews coefficient Solvent content 3 58.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.97 α = 90 b = 101.97 β = 90 c = 151.617 γ = 90
Symmetry Space Group P 41 21 2
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 EIGER2 S 9M 2021-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL02U1 1 SSRF BL02U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 3 45.32 97.91 0.02245 0.03175 0.02245 1 15.77 2 16618
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.107 0.3028 0.4283 0.3028 0.894 2.33
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 1W98 3 45.32 15514 797 98.08 0.25409 0.24867 0.2532 0.35788 0.3685 RANDOM 86.146
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] 4.58 4.58 -9.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.421 r_dihedral_angle_3_deg 21.217 r_long_range_B_refined 16.085 r_long_range_B_other 16.083 r_dihedral_angle_4_deg 15.926 r_mcangle_it 13.08 r_mcangle_other 13.079 r_scangle_other 11.852 r_mcbond_it 8.784 r_mcbond_other 8.771
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.421 r_dihedral_angle_3_deg 21.217 r_long_range_B_refined 16.085 r_long_range_B_other 16.083 r_dihedral_angle_4_deg 15.926 r_mcangle_it 13.08 r_mcangle_other 13.079 r_scangle_other 11.852 r_mcbond_it 8.784 r_mcbond_other 8.771 r_dihedral_angle_1_deg 8.137 r_scbond_it 7.742 r_scbond_other 7.741 r_angle_refined_deg 1.689 r_angle_other_deg 1.199 r_chiral_restr 0.071 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001 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 Atoms Number Protein Atoms 4627 Nucleic Acid Atoms Solvent Atoms 2 Heterogen Atoms 24
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction PHENIX phasing