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Structure of the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase reduced by sodium dithionite (sulfite complex)
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 8.7 278 Protein solution (5mcl): 14.5mg/ml TvNiR, 0.005M Tris borate (pH8.7). Reservoir solution (5mcl): 0.2M tri-sodium citrate dihydrate, 0.1M Tris hydrochloride (pH8.5), 30% v/v PEG400, VAPOR DIFFUSION, HANGING DROP, temperature 278.0K
Crystal Properties Matthews coefficient Solvent content 4.06 69.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 193.79 α = 90 b = 193.79 β = 90 c = 193.79 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 IMAGE PLATE MAR scanner 345 mm plate 2004-11-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7B 0.843 EMBL/DESY, HAMBURG BW7B
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 1.4 12 99.7 0.055 33.1 469642 468027
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 1.4 1.42 100 0.547 2.7
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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2OT4 1.4 12 443992 23479 99.38 0.12663 0.12595 0.1274 0.13946 0.141 RANDOM 17.514
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 36.27 r_dihedral_angle_4_deg 16.213 r_dihedral_angle_3_deg 12.076 r_sphericity_free 7.641 r_dihedral_angle_1_deg 5.954 r_sphericity_bonded 3.834 r_scangle_it 3.358 r_scbond_it 2.445 r_mcangle_it 1.821 r_angle_refined_deg 1.558
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.27 r_dihedral_angle_4_deg 16.213 r_dihedral_angle_3_deg 12.076 r_sphericity_free 7.641 r_dihedral_angle_1_deg 5.954 r_sphericity_bonded 3.834 r_scangle_it 3.358 r_scbond_it 2.445 r_mcangle_it 1.821 r_angle_refined_deg 1.558 r_rigid_bond_restr 1.385 r_mcbond_it 1.232 r_angle_other_deg 0.973 r_mcbond_other 0.708 r_symmetry_vdw_other 0.327 r_nbd_refined 0.22 r_nbd_other 0.214 r_nbtor_refined 0.207 r_symmetry_vdw_refined 0.18 r_symmetry_metal_ion_refined 0.15 r_symmetry_hbond_refined 0.123 r_metal_ion_refined 0.116 r_nbtor_other 0.112 r_xyhbond_nbd_refined 0.112 r_chiral_restr 0.095 r_bond_refined_d 0.018 r_gen_planes_refined 0.016 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8217 Nucleic Acid Atoms Solvent Atoms 1385 Heterogen Atoms 922
Software Software Software Name Purpose HKL-2000 data collection REFMAC refinement DENZO data reduction SCALEPACK data scaling