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Crystal structure of CDK2 IN complex with Inhibitor NU-6140
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3QXP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 0.1M Tris pH 8.0, 0.1M NaCl, 20% PEG monomethyl ether 550
Crystal Properties Matthews coefficient Solvent content 2.04 39.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.491 α = 90 b = 72.01 β = 90 c = 72.33 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 CCD Nonius Kappa CCD mirrors 2018-10-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 1.0 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.3 53.01 99.5 0.098 9.6 6.6 12976
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.38 95.6 0.57 2.2 6.6
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 3QXP 2.3 51.03 12283 653 99.39 0.2179 0.21386 0.2231 0.29036 0.2878 RANDOM 41.699
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] 0.02 0.02 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 45.143 r_dihedral_angle_3_deg 18.594 r_dihedral_angle_4_deg 18.233 r_long_range_B_other 9.553 r_long_range_B_refined 9.504 r_scangle_other 6.924 r_dihedral_angle_1_deg 6.613 r_mcangle_it 4.345 r_scbond_other 3.871 r_scbond_it 3.597
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 45.143 r_dihedral_angle_3_deg 18.594 r_dihedral_angle_4_deg 18.233 r_long_range_B_other 9.553 r_long_range_B_refined 9.504 r_scangle_other 6.924 r_dihedral_angle_1_deg 6.613 r_mcangle_it 4.345 r_scbond_other 3.871 r_scbond_it 3.597 r_mcbond_it 2.724 r_angle_refined_deg 1.728 r_angle_other_deg 1.02 r_chiral_restr 0.117 r_gen_planes_other 0.033 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_bond_other_d 0.004 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_mcbond_other r_mcangle_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 2245 Nucleic Acid Atoms Solvent Atoms 48 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALEPACK data scaling MOLREP phasing