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Crystal structure of cytochrome c nitrite reductase NrfHA complex bound to the HQNO inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2J7A PDB ENTRY 2J7A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7 277 277 K 9% PEG 4K 0.1 M HEPES PH 7.5 100 MM GLYCYL-GLYCYL-GLYCINE VAPOUR DIFFUSION METHOD.
Crystal Properties Matthews coefficient Solvent content 3.5 65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.102 α = 90 b = 189.115 β = 90 c = 263.46 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 ADSC CCD 2006-09-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.8 29.77 86.5 0.11 9.4 2.8 92571 2
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 2.8 2.9 75.4 0.38 2.5 2.5
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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2J7A 2.8 154.3 83976 2592 87 0.221 0.22 0.2153 0.261 0.2526 RANDOM 24.61
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] -2.5 0.88 1.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.599 r_dihedral_angle_4_deg 18.826 r_dihedral_angle_3_deg 18.013 r_dihedral_angle_1_deg 5.878 r_scangle_it 1.506 r_angle_refined_deg 1.421 r_scbond_it 0.961 r_mcangle_it 0.508 r_nbtor_refined 0.305 r_mcbond_it 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.599 r_dihedral_angle_4_deg 18.826 r_dihedral_angle_3_deg 18.013 r_dihedral_angle_1_deg 5.878 r_scangle_it 1.506 r_angle_refined_deg 1.421 r_scbond_it 0.961 r_mcangle_it 0.508 r_nbtor_refined 0.305 r_mcbond_it 0.301 r_symmetry_vdw_refined 0.28 r_nbd_refined 0.265 r_xyhbond_nbd_refined 0.141 r_metal_ion_refined 0.137 r_chiral_restr 0.094 r_symmetry_hbond_refined 0.056 r_bond_refined_d 0.013 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other 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_other r_long_range_B_refined 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 18217 Nucleic Acid Atoms Solvent Atoms 114 Heterogen Atoms 1250
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing