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Complex structure of CDK2/Cyclin E1 and a potent, selective macrocyclic 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 59.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.588 α = 90 b = 101.588 β = 90 c = 152.425 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 2.44 45.43 99.82 0.01171 0.01657 0.01171 1 19.08 2 30394
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 2.44 2.527 0.3031 0.4286 0.3031 0.832 2.34
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 2.44 45.43 30394 1574 99.82 0.22207 0.2211 0.2254 0.2924 0.2957 RANDOM 78.41
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] 1.5 1.5 -2.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.781 r_dihedral_angle_4_deg 19.104 r_dihedral_angle_3_deg 18.813 r_long_range_B_other 13.746 r_long_range_B_refined 13.742 r_scangle_other 10.454 r_mcangle_it 10.3 r_mcangle_other 10.299 r_dihedral_angle_1_deg 7.603 r_mcbond_it 7.295
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.781 r_dihedral_angle_4_deg 19.104 r_dihedral_angle_3_deg 18.813 r_long_range_B_other 13.746 r_long_range_B_refined 13.742 r_scangle_other 10.454 r_mcangle_it 10.3 r_mcangle_other 10.299 r_dihedral_angle_1_deg 7.603 r_mcbond_it 7.295 r_mcbond_other 7.284 r_scbond_it 7.265 r_scbond_other 7.264 r_angle_refined_deg 1.626 r_angle_other_deg 1.247 r_chiral_restr 0.073 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 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 4623 Nucleic Acid Atoms Solvent Atoms 50 Heterogen Atoms 27
Software Software Software Name Purpose SCALEPACK data scaling PHENIX refinement PDB_EXTRACT data extraction HKL-2000 data reduction PHENIX phasing