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Bub1 kinase domain in complex with covalent inhibitor BM047
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4QPM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M HEPES pH 7.0, 20% PEG3350, 0.1 M calcium chloride
Crystal Properties Matthews coefficient Solvent content 2.23 44.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.394 α = 90 b = 115.969 β = 90 c = 124.679 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 PILATUS3 6M 2023-07-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.965 ESRF MASSIF-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 2.3 47.52 98.3 0.998 11.5 3.9 33190
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 2.3 2.38 0.703
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 2.3 42.494 33150 913 97.589 0.201 0.1995 0.2093 0.2486 0.2491 66.306
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] 0.323 -5.617 5.294
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.875 r_dihedral_angle_3_deg 13.336 r_lrange_other 10.784 r_lrange_it 10.783 r_dihedral_angle_2_deg 10.019 r_dihedral_angle_1_deg 7.237 r_scangle_it 7.131 r_scangle_other 7.13 r_mcangle_it 5.487 r_mcangle_other 5.487
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.875 r_dihedral_angle_3_deg 13.336 r_lrange_other 10.784 r_lrange_it 10.783 r_dihedral_angle_2_deg 10.019 r_dihedral_angle_1_deg 7.237 r_scangle_it 7.131 r_scangle_other 7.13 r_mcangle_it 5.487 r_mcangle_other 5.487 r_scbond_it 4.798 r_scbond_other 4.797 r_mcbond_it 3.73 r_mcbond_other 3.73 r_angle_refined_deg 1.539 r_angle_other_deg 0.518 r_symmetry_xyhbond_nbd_refined 0.388 r_symmetry_nbd_refined 0.242 r_nbd_refined 0.214 r_symmetry_nbd_other 0.192 r_nbtor_refined 0.187 r_xyhbond_nbd_refined 0.182 r_nbd_other 0.166 r_ncsr_local_group_1 0.085 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.071 r_symmetry_xyhbond_nbd_other 0.067 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5597 Nucleic Acid Atoms Solvent Atoms 91 Heterogen Atoms 82
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing PDB-REDO refinement