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Bub1 kinase domain in complex with inhibitor LEI221
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, 18% PEG3350, 0.1 M calcium chloride
Crystal Properties Matthews coefficient Solvent content 2.27 45.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.579 α = 90 b = 50.105 β = 101.962 c = 114.015 γ = 90
Symmetry Space Group P 1 21 1
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 2024-04-27 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 1.85 111.54 95.3 0.998 14.2 2.1 61085
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 1.85 1.89 0.667
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 1.85 66.2 61078 3026 95.167 0.188 0.1864 0.1955 0.2235 0.2297 46.675
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] 1.125 -0.613 -0.318 -0.502
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 21.052 r_dihedral_angle_6_deg 15.388 r_lrange_other 13.946 r_lrange_it 13.91 r_scangle_it 13.155 r_scangle_other 13.154 r_dihedral_angle_3_deg 12.145 r_scbond_other 11.502 r_scbond_it 11.501 r_dihedral_angle_other_2_deg 8.742
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 21.052 r_dihedral_angle_6_deg 15.388 r_lrange_other 13.946 r_lrange_it 13.91 r_scangle_it 13.155 r_scangle_other 13.154 r_dihedral_angle_3_deg 12.145 r_scbond_other 11.502 r_scbond_it 11.501 r_dihedral_angle_other_2_deg 8.742 r_mcangle_other 8.513 r_mcangle_it 8.51 r_mcbond_it 7.65 r_mcbond_other 7.647 r_dihedral_angle_1_deg 5.497 r_angle_refined_deg 1.346 r_angle_other_deg 0.449 r_nbd_refined 0.212 r_symmetry_nbd_refined 0.199 r_symmetry_nbd_other 0.191 r_nbtor_refined 0.185 r_symmetry_xyhbond_nbd_refined 0.182 r_nbd_other 0.18 r_xyhbond_nbd_refined 0.169 r_symmetry_xyhbond_nbd_other 0.141 r_metal_ion_refined 0.106 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.066 r_ncsr_local_group_1 0.063 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 5409 Nucleic Acid Atoms Solvent Atoms 296 Heterogen Atoms 100
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing PDB-REDO refinement