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Crystal structure of human NQO1 in complex with the inhibitor PMSF
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5A4K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 291.15 0.1 M Tris pH 8.5, 0.2 M Sodium Acetate, 20% polyethylene glycol 3350
Crystal Properties Matthews coefficient Solvent content 2.32 47.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.172 α = 90 b = 58.928 β = 98.93 c = 189.161 γ = 90
Symmetry Space Group I 1 2 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 PILATUS 6M 2021-12-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.98 ALBA XALOC
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 1.6 49.52 99.5 0.999 11.7 6.6 135910
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 1.6 1.64 94.3 0.076
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 1.6 49.47 135910 15129 98.13 0.21178 0.20788 0.2154 0.24654 0.2538 RANDOM 32.967
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.267 r_long_range_B_other 8.869 r_long_range_B_refined 8.839 r_dihedral_angle_1_deg 6.498 r_dihedral_angle_2_deg 5.995 r_scangle_other 5.779 r_mcangle_it 4.167 r_mcangle_other 4.167 r_scbond_it 3.663 r_scbond_other 3.663
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.267 r_long_range_B_other 8.869 r_long_range_B_refined 8.839 r_dihedral_angle_1_deg 6.498 r_dihedral_angle_2_deg 5.995 r_scangle_other 5.779 r_mcangle_it 4.167 r_mcangle_other 4.167 r_scbond_it 3.663 r_scbond_other 3.663 r_mcbond_it 2.932 r_mcbond_other 2.932 r_angle_refined_deg 1.42 r_angle_other_deg 0.53 r_chiral_restr 0.077 r_gen_planes_refined 0.008 r_bond_refined_d 0.007 r_bond_other_d 0.003 r_gen_planes_other 0.002 r_dihedral_angle_4_deg 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 8913 Nucleic Acid Atoms Solvent Atoms 1016 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing