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Structure of a hexameric multiheme c nitrite reductase from the extremophile bacterium Thiolkalivibrio paradoxus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OT4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 free-interface-diffusion technique 6.5 278 14 mg/mL protein, 0.02M cobalt chloride, 0.1M MES (pH 6.5), 2.8 M ammonium sulfate, free-interface-diffusion technique, temperature 278.0K
Crystal Properties Matthews coefficient Solvent content 5.11 75.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 193.64 α = 90 b = 193.64 β = 90 c = 193.64 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 2010-12-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 0.800 SPring-8 BL41XU
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 1.9 29.9 98.9 0.098 9.47 188857 186813 23.8
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 1.9 2 99.7 0.521 2.24 26633
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 2OT4 1.9 29.9 177340 9466 98.92 0.1394 0.1382 0.1394 0.16205 0.1635 RANDOM 15.556
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 35.351 r_dihedral_angle_4_deg 15.506 r_dihedral_angle_3_deg 12.712 r_dihedral_angle_1_deg 6.311 r_angle_refined_deg 1.493 r_scangle_it 1.197 r_mcangle_it 0.9 r_scbond_it 0.725 r_mcbond_it 0.487 r_chiral_restr 0.108
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.351 r_dihedral_angle_4_deg 15.506 r_dihedral_angle_3_deg 12.712 r_dihedral_angle_1_deg 6.311 r_angle_refined_deg 1.493 r_scangle_it 1.197 r_mcangle_it 0.9 r_scbond_it 0.725 r_mcbond_it 0.487 r_chiral_restr 0.108 r_bond_refined_d 0.02 r_gen_planes_refined 0.014
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8181 Nucleic Acid Atoms Solvent Atoms 1284 Heterogen Atoms 766
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling