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Crystal structure of Cyclin-dependent kinase 2/cyclin A in complex with 3,5,7-Substituted pyrazolo[4,3-d]pyrimidine inhibitor 24
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7B7S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 291.15 70%: 10% w/v PEG 4,000, 20% v/v glycerol, 0.03 M NaNO3, 0.03 M Na2HPO4, 0.03 M (NH4)2SO4, 0.1 M Tris/Bicine pH 8.5
30%:20% w/v PEG 6000, 0.1 M Bicine, pH 9
Crystal Properties Matthews coefficient Solvent content 3.15 60.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.89 α = 90 b = 163.9 β = 106.61 c = 73.17 γ = 90
Symmetry Space Group P 1 21 1
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 PILATUS3 6M 2021-03-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.7 46.96 97.3 0.172 0.185 0.998 10.77 7.023 168531 30.849
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.8 95.3 1.974 2.136 0.482 0.97 6.778
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 7B7S 1.7 46.96 166428 2100 97.41 0.2004 0.2001 0.2089 0.2236 0.2305 RANDOM 31.558
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.758 r_dihedral_angle_4_deg 16.433 r_dihedral_angle_3_deg 13.619 r_dihedral_angle_1_deg 5.894 r_angle_other_deg 2.262 r_angle_refined_deg 1.571 r_chiral_restr 0.084 r_bond_other_d 0.033 r_bond_refined_d 0.017 r_gen_planes_other 0.013
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.758 r_dihedral_angle_4_deg 16.433 r_dihedral_angle_3_deg 13.619 r_dihedral_angle_1_deg 5.894 r_angle_other_deg 2.262 r_angle_refined_deg 1.571 r_chiral_restr 0.084 r_bond_other_d 0.033 r_bond_refined_d 0.017 r_gen_planes_other 0.013 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8761 Nucleic Acid Atoms Solvent Atoms 969 Heterogen Atoms 135
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing PDB_EXTRACT data extraction