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Structure of the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase in a complex with nitrite (full occupancy)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OT4 PDB ENTRY 2OT4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 278 Protein solution (2.5 uL): 11.6 mg/mL TvNiR, 0.05 M Tris-HCl, pH 8.0, reservoir solution (2.5 uL): 0.2 M ammonium acetate, 0.1 M citric acid trisodium salt, pH 5.6, 30% MPD, 0.1 M sodium nitrite, VAPOR DIFFUSION, HANGING DROP, temperature 278.0K
Crystal Properties Matthews coefficient Solvent content 5.066891 75.724762
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 192.8 α = 90 b = 192.8 β = 90 c = 192.8 γ = 90
Symmetry Space Group P 21 3
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 MAR CCD 165 mm 2010-06-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON KURCHATOV SNC BEAMLINE K4.4 KURCHATOV SNC K4.4
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 1.83 136.33 99.8 0.12 20 208153 26.2
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 1.83 1.9 99.9 0.671 3.9
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 2OT4 1.83 100 197647 10466 99.85 0.14239 0.14137 0.1446 0.16196 0.1646 RANDOM 21.013
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_2_deg 36.999 r_dihedral_angle_4_deg 18.945 r_dihedral_angle_3_deg 12.468 r_dihedral_angle_1_deg 6.294 r_scangle_it 3.544 r_scbond_it 2.325 r_angle_refined_deg 1.7 r_mcangle_it 1.498 r_mcbond_it 0.874 r_chiral_restr 0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.999 r_dihedral_angle_4_deg 18.945 r_dihedral_angle_3_deg 12.468 r_dihedral_angle_1_deg 6.294 r_scangle_it 3.544 r_scbond_it 2.325 r_angle_refined_deg 1.7 r_mcangle_it 1.498 r_mcbond_it 0.874 r_chiral_restr 0.11 r_bond_refined_d 0.02 r_gen_planes_refined 0.016 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8239 Nucleic Acid Atoms Solvent Atoms 1327 Heterogen Atoms 712
Software Software Software Name Purpose AUTOMAR data collection REFMAC refinement XDS data reduction XSCALE data scaling