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Crystal structure of BAY 1000394 (Roniciclib) bound to CDK2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.8 293.15 7.25% PEG 4000, 0.2M ammonium acetate, 100mM Hepes pH 7.8
Crystal Properties Matthews coefficient Solvent content 2.07 40.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.776 α = 90 b = 71.814 β = 90 c = 72.901 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 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.918 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.03 43.28 95.9 12.05 3.59 17101
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 (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 2.03 43.28 17101 901 95.5 0.19843 0.19515 0.2192 0.2615 0.2791 RANDOM 21.564
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] -0.3 -2.97 3.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.317 r_dihedral_angle_3_deg 16.77 r_dihedral_angle_4_deg 16.728 r_long_range_B_refined 6.832 r_long_range_B_other 6.805 r_dihedral_angle_1_deg 6.17 r_scangle_other 2.951 r_mcangle_it 2.645 r_mcangle_other 2.645 r_angle_refined_deg 1.892
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.317 r_dihedral_angle_3_deg 16.77 r_dihedral_angle_4_deg 16.728 r_long_range_B_refined 6.832 r_long_range_B_other 6.805 r_dihedral_angle_1_deg 6.17 r_scangle_other 2.951 r_mcangle_it 2.645 r_mcangle_other 2.645 r_angle_refined_deg 1.892 r_scbond_it 1.835 r_scbond_other 1.835 r_mcbond_it 1.631 r_mcbond_other 1.631 r_angle_other_deg 0.911 r_chiral_restr 0.106 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 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 2309 Nucleic Acid Atoms Solvent Atoms 154 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing