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Structure of the human quinone reductase 2 (NQO2) in complex with imiquimod
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BZS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 0.1 M Tris HCl pH 8.5
2 M ammonium sulphate
Crystal Properties Matthews coefficient Solvent content 2.31 46.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.689 α = 90 b = 80.925 β = 90 c = 106.198 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 2016-04-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.976 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.75 44.4 93 0.124 0.995 6.01 4.6 49249
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 1.75 1.81 75 1.6 0.05 4.7
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 FOURIER SYNTHESIS THROUGHOUT 2BZS 1.75 44.4 45013 2372 93.27 0.19909 0.19765 0.209 0.22652 0.2359 RANDOM 27.413
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] 1.77 0.03 -1.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.75 r_dihedral_angle_4_deg 16.838 r_dihedral_angle_3_deg 11.868 r_dihedral_angle_1_deg 6.321 r_long_range_B_refined 4.587 r_long_range_B_other 4.544 r_angle_refined_deg 1.716 r_scangle_other 1.256 r_mcangle_it 1.046 r_mcangle_other 1.046
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.75 r_dihedral_angle_4_deg 16.838 r_dihedral_angle_3_deg 11.868 r_dihedral_angle_1_deg 6.321 r_long_range_B_refined 4.587 r_long_range_B_other 4.544 r_angle_refined_deg 1.716 r_scangle_other 1.256 r_mcangle_it 1.046 r_mcangle_other 1.046 r_angle_other_deg 0.975 r_scbond_it 0.85 r_scbond_other 0.769 r_mcbond_it 0.623 r_mcbond_other 0.619 r_chiral_restr 0.097 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 3599 Nucleic Acid Atoms Solvent Atoms 221 Heterogen Atoms 195
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling REFMAC phasing