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Quinol-dependent nitric oxide reductase (qNOR) from Neisseria meningitidis in the monomeric oxidized state with zinc complex.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 277 50 mM HEPES pH8
26% PEG 600 (v/v)
0.5 mM zinc sulphate
Crystal Properties Matthews coefficient Solvent content 4.17 70.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.12 α = 90 b = 116.68 β = 90 c = 123.55 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 CCD RAYONIX MX300HE 2017-05-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 3.1 49.92 83.3 0.113 0.141 0.064 0.997 6.5 4.1 19034 61
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.1 3.31 84.5 0.556 0.7 0.42 0.284 2.2 4
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 MIR THROUGHOUT 3.15 49.92 19034 1063 81.46 0.25313 0.25029 0.2514 0.30253 0.304 RANDOM 100.951
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] -5.94 0.18 5.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.285 r_dihedral_angle_3_deg 19.755 r_dihedral_angle_4_deg 14.511 r_long_range_B_refined 13.719 r_mcangle_it 8.12 r_dihedral_angle_1_deg 6.296 r_scbond_it 5.069 r_mcbond_it 4.881 r_angle_refined_deg 0.999 r_chiral_restr 0.085
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.285 r_dihedral_angle_3_deg 19.755 r_dihedral_angle_4_deg 14.511 r_long_range_B_refined 13.719 r_mcangle_it 8.12 r_dihedral_angle_1_deg 6.296 r_scbond_it 5.069 r_mcbond_it 4.881 r_angle_refined_deg 0.999 r_chiral_restr 0.085 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5562 Nucleic Acid Atoms Solvent Atoms 1 Heterogen Atoms 91
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction Aimless data scaling MOLREP phasing