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Structure of the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase in a complex with azide
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 8.5 278 The drop contained 5ml of enzyme solution (14.5mg/ml) in 0.005M Tris-borat buffer (PH8.7) and 5ml reservoir solution. the reservoir solution contained 27% PEG400, 0.18M sodium citrate in 0.09M TRIS buffer (PH8.5), Complex with azide ion was obtained by soaking crystal in reservoir solution with 20mM sodium azide by 30 minute, VAPOR DIFFUSION, HANGING DROP, temperature 278K
Crystal Properties Matthews coefficient Solvent content 5.04 75.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 193.027 α = 90 b = 193.027 β = 90 c = 193.027 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 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 EMBL/DESY, HAMBURG X13
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 1.7 13 98.6 0.058 21 270000
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 1.7 1.71 98.3 0.489
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 1.7 11.99 243353 12944 98.37 0.1521 0.15128 0.1541 0.16763 0.1692 RANDOM 16.487
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 36.318 r_dihedral_angle_4_deg 17.321 r_dihedral_angle_3_deg 12.258 r_dihedral_angle_1_deg 6.013 r_scangle_it 3.039 r_scbond_it 1.971 r_angle_refined_deg 1.519 r_mcangle_it 1.287 r_angle_other_deg 0.947 r_mcbond_it 0.754
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.318 r_dihedral_angle_4_deg 17.321 r_dihedral_angle_3_deg 12.258 r_dihedral_angle_1_deg 6.013 r_scangle_it 3.039 r_scbond_it 1.971 r_angle_refined_deg 1.519 r_mcangle_it 1.287 r_angle_other_deg 0.947 r_mcbond_it 0.754 r_symmetry_vdw_other 0.297 r_symmetry_vdw_refined 0.285 r_symmetry_metal_ion_refined 0.236 r_mcbond_other 0.231 r_nbd_refined 0.224 r_nbd_other 0.211 r_nbtor_refined 0.188 r_xyhbond_nbd_refined 0.123 r_symmetry_hbond_refined 0.121 r_nbtor_other 0.093 r_chiral_restr 0.088 r_metal_ion_refined 0.087 r_bond_refined_d 0.018 r_gen_planes_refined 0.014 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8228 Nucleic Acid Atoms Solvent Atoms 1124 Heterogen Atoms 817
Software Software Software Name Purpose MOLREP phasing REFMAC refinement HKL-2000 data collection DENZO data reduction SCALEPACK data scaling