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Discovery of (4-Pyrazolyl)-2-Aminopyrimidines as Potent and Selective Inhibitors of Cyclin-Dependent Kinase 2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other proprietary structure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 0.1 M Tris pH 8.5, 16% PEG 2000 MME, 0.2 M trimethylamine N-oxide
Crystal Properties Matthews coefficient Solvent content 2.04 39.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.663 α = 90 b = 72.009 β = 90 c = 71.913 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 EIGER X 16M 2021-07-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.9763 MAX IV BioMAX
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.4 43.01 99.8 0.07 0.02 0.997 16.2 13.4 55105 21.52
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.4 1.43 99.5 1.54 0.43 0.892 2.2 13.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.55 43.004 41140 2096 99.917 0.158 0.155 0.1552 0.2034 0.2029 27.907
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] -0.608 -0.603 1.211
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.043 r_dihedral_angle_3_deg 13.402 r_dihedral_angle_2_deg 13.296 r_rigid_bond_restr 6.804 r_dihedral_angle_1_deg 6.237 r_scangle_it 5.21 r_scangle_other 5.208 r_lrange_other 5.081 r_lrange_it 5.08 r_mcangle_it 4.586
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.043 r_dihedral_angle_3_deg 13.402 r_dihedral_angle_2_deg 13.296 r_rigid_bond_restr 6.804 r_dihedral_angle_1_deg 6.237 r_scangle_it 5.21 r_scangle_other 5.208 r_lrange_other 5.081 r_lrange_it 5.08 r_mcangle_it 4.586 r_mcangle_other 4.585 r_scbond_it 4.574 r_scbond_other 4.572 r_mcbond_it 3.974 r_mcbond_other 3.974 r_angle_refined_deg 1.863 r_angle_other_deg 0.739 r_nbd_refined 0.224 r_nbtor_refined 0.175 r_symmetry_nbd_other 0.163 r_symmetry_nbd_refined 0.163 r_symmetry_xyhbond_nbd_refined 0.161 r_nbd_other 0.139 r_xyhbond_nbd_refined 0.119 r_chiral_restr 0.099 r_symmetry_nbtor_other 0.073 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 r_bond_other_d 0.003 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2132 Nucleic Acid Atoms Solvent Atoms 122 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement XDS data reduction STARANISO data scaling DIMPLE phasing