☰ Navigation Tabs
Structure of the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase in a complex with nitrite
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 nitrite ion was obtained by soaking crystal in reservoir solution with 100mM sodium nitrite by 30 minute, VAPOR DIFFUSION, HANGING DROP, temperature 278K
Crystal Properties Matthews coefficient Solvent content 5.07 75.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 193.412 α = 90 b = 193.412 β = 90 c = 193.412 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 1.8 13 99.7 0.079 16 228600
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 1.8 1.82 98.8 0.6
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 1.8 11.99 208802 11051 99.47 0.14936 0.1485 0.1514 0.16547 0.1673 RANDOM 16.63
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 36.367 r_dihedral_angle_4_deg 18.029 r_dihedral_angle_3_deg 12.419 r_dihedral_angle_1_deg 6.127 r_scangle_it 3.368 r_scbond_it 2.238 r_angle_refined_deg 1.641 r_mcangle_it 1.408 r_angle_other_deg 1.049 r_mcbond_it 0.841
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.367 r_dihedral_angle_4_deg 18.029 r_dihedral_angle_3_deg 12.419 r_dihedral_angle_1_deg 6.127 r_scangle_it 3.368 r_scbond_it 2.238 r_angle_refined_deg 1.641 r_mcangle_it 1.408 r_angle_other_deg 1.049 r_mcbond_it 0.841 r_symmetry_vdw_other 0.301 r_mcbond_other 0.271 r_nbd_refined 0.223 r_nbd_other 0.215 r_nbtor_refined 0.19 r_xyhbond_nbd_refined 0.141 r_symmetry_hbond_refined 0.139 r_symmetry_vdw_refined 0.118 r_chiral_restr 0.114 r_symmetry_metal_ion_refined 0.095 r_nbtor_other 0.094 r_metal_ion_refined 0.078 r_bond_refined_d 0.021 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 8225 Nucleic Acid Atoms Solvent Atoms 1130 Heterogen Atoms 767
Software Software Software Name Purpose MOLREP phasing REFMAC refinement HKL-2000 data collection DENZO data reduction SCALEPACK data scaling