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Structure of a hexameric multiheme c nitrite reductase from the extremophile bacterium Thiolkalivibrio nitratireducens
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 278 The drop contained 5mkl of enzyme solution (14.5 mg/ml) in 0.005 M Tris-borat buffer (pH 8.7) and 5 mkl reservoir solution. The reservoir solution contained 26.3% MPD, 0.175 M ammonium acetate in 0.09 M sodium citrate buffer (pH 5.6), VAPOR DIFFUSION, HANGING DROP, temperature 278K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 193.917 α = 90 b = 193.917 β = 90 c = 193.917 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 BW7A 0.96, 1.7375 EMBL/DESY, HAMBURG BW7A
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 1.5 30 97.4 0.036 17.1 373791 17.1
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) 1.5 1.52 98.3 0.476 12460
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 1.5 24.04 373155 11295 100 0.127 0.126 0.1279 0.141 0.1424 RANDOM 15.294
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 36.138 r_dihedral_angle_4_deg 17.981 r_dihedral_angle_3_deg 12.279 r_sphericity_free 7.897 r_dihedral_angle_1_deg 6.143 r_sphericity_bonded 3.902 r_scangle_it 3.561 r_scbond_it 2.685 r_mcangle_it 1.903 r_angle_refined_deg 1.575
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.138 r_dihedral_angle_4_deg 17.981 r_dihedral_angle_3_deg 12.279 r_sphericity_free 7.897 r_dihedral_angle_1_deg 6.143 r_sphericity_bonded 3.902 r_scangle_it 3.561 r_scbond_it 2.685 r_mcangle_it 1.903 r_angle_refined_deg 1.575 r_rigid_bond_restr 1.423 r_mcbond_it 1.377 r_angle_other_deg 1.093 r_mcbond_other 0.692 r_symmetry_vdw_other 0.303 r_nbd_refined 0.222 r_nbd_other 0.204 r_nbtor_refined 0.192 r_symmetry_hbond_refined 0.191 r_symmetry_vdw_refined 0.141 r_xyhbond_nbd_refined 0.139 r_chiral_restr 0.096 r_nbtor_other 0.09 r_metal_ion_refined 0.032 r_bond_refined_d 0.019 r_gen_planes_refined 0.015 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8228 Nucleic Acid Atoms Solvent Atoms 1217 Heterogen Atoms 759
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection SHELXS phasing