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Crystal structure of octaheme nitrite reductase from Trichlorobacter ammonificans in space group P63
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3UU9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.7 293 17-20 % PEG 3350, 0.1 M Bis-Tris
Crystal Properties Matthews coefficient Solvent content 2.2 44.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.2 α = 90 b = 114.2 β = 90 c = 64.8 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 12M 2018-11-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.97242 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 1.6 98.9 99.9 0.888 14.6 11.3 59330
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.74 0.656
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.6 98.9 59330 2709 99.902 0.197 0.1942 0.1995 0.2433 0.1961 21.496
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] -0.507 -0.254 -0.507 1.646
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.6 r_dihedral_angle_3_deg 15.556 r_dihedral_angle_4_deg 14.312 r_dihedral_angle_other_3_deg 11.739 r_dihedral_angle_1_deg 7.297 r_lrange_it 4.675 r_lrange_other 4.597 r_scangle_it 3.137 r_scangle_other 3.134 r_angle_refined_deg 2.794
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.6 r_dihedral_angle_3_deg 15.556 r_dihedral_angle_4_deg 14.312 r_dihedral_angle_other_3_deg 11.739 r_dihedral_angle_1_deg 7.297 r_lrange_it 4.675 r_lrange_other 4.597 r_scangle_it 3.137 r_scangle_other 3.134 r_angle_refined_deg 2.794 r_mcangle_it 2.683 r_mcangle_other 2.683 r_scbond_it 2.079 r_scbond_other 2.077 r_mcbond_it 1.849 r_mcbond_other 1.841 r_angle_other_deg 1.553 r_nbd_refined 0.203 r_symmetry_nbd_other 0.186 r_symmetry_xyhbond_nbd_refined 0.173 r_nbtor_refined 0.166 r_chiral_restr 0.161 r_symmetry_nbd_refined 0.158 r_xyhbond_nbd_refined 0.147 r_nbd_other 0.139 r_symmetry_xyhbond_nbd_other 0.133 r_metal_ion_refined 0.095 r_symmetry_nbtor_other 0.093 r_gen_planes_other 0.016 r_bond_refined_d 0.015 r_gen_planes_refined 0.014 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3891 Nucleic Acid Atoms Solvent Atoms 505 Heterogen Atoms 350
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling XDS data reduction MOLREP phasing