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CDK2/cyclin A2 in complex with pyrazolo[4,3-d]pyrimidine inhibitor LGR6768
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6GVA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 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%:0.8 M sodium phosphate monobasic monohydrate, 0.8 M potassium phosphate monobasic, 0.1 M Sodium HEPES, pH7.5
Crystal Properties Matthews coefficient Solvent content 3.17 61.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.023 α = 90 b = 134.978 β = 90 c = 163.963 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 2020-10-22 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) 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 2.6 50 99.9 0.988 5.42 13.6 50620 39.44
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.76 0.717 1.01
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 6GVA 2.6 49.56 49156 1460 99.9 0.2344 0.2328 0.2403 0.2874 0.2882 RANDOM 39.612
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] 0.07 -0.12 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.726 r_dihedral_angle_4_deg 17.942 r_dihedral_angle_3_deg 14.355 r_dihedral_angle_1_deg 7.033 r_angle_other_deg 2.237 r_angle_refined_deg 1.596 r_chiral_restr 0.071 r_bond_other_d 0.034 r_bond_refined_d 0.011 r_gen_planes_other 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.726 r_dihedral_angle_4_deg 17.942 r_dihedral_angle_3_deg 14.355 r_dihedral_angle_1_deg 7.033 r_angle_other_deg 2.237 r_angle_refined_deg 1.596 r_chiral_restr 0.071 r_bond_other_d 0.034 r_bond_refined_d 0.011 r_gen_planes_other 0.01 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8828 Nucleic Acid Atoms Solvent Atoms 314 Heterogen Atoms 98
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling