☰ Navigation Tabs
Crystal structure of octaheme nitrite reductase from Trichlorobacter ammonificans in space group P21
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 5.7 278 17-20 % PEG 3350, 0.1 M Bis-Tris
Crystal Properties Matthews coefficient Solvent content 2.2 44.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.2 α = 90 b = 64.8 β = 119.9 c = 114.2 γ = 90
Symmetry Space Group P 1 21 1
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 1.737 42.877 98 0.996 10.7 4.2 145919
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.737 1.83 0.956 0.844
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 FREE R-VALUE 1.737 42.877 145919 7348 97.76 0.195 0.1913 0.1964 0.2542 0.2607 21.354
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] -2.737 5.607 9.76 -7.023
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.525 r_dihedral_angle_3_deg 19.199 r_dihedral_angle_4_deg 16.883 r_dihedral_angle_other_3_deg 12.447 r_dihedral_angle_1_deg 8.494 r_lrange_it 3.976 r_lrange_other 3.951 r_angle_refined_deg 3.056 r_mcangle_it 2.893 r_mcangle_other 2.893
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.525 r_dihedral_angle_3_deg 19.199 r_dihedral_angle_4_deg 16.883 r_dihedral_angle_other_3_deg 12.447 r_dihedral_angle_1_deg 8.494 r_lrange_it 3.976 r_lrange_other 3.951 r_angle_refined_deg 3.056 r_mcangle_it 2.893 r_mcangle_other 2.893 r_scangle_it 2.603 r_scangle_other 2.601 r_mcbond_it 2.181 r_mcbond_other 2.181 r_scbond_it 1.97 r_scbond_other 1.969 r_angle_other_deg 1.445 r_symmetry_xyhbond_nbd_refined 0.218 r_xyhbond_nbd_refined 0.215 r_nbd_refined 0.213 r_nbd_other 0.212 r_symmetry_nbd_other 0.204 r_symmetry_nbd_refined 0.198 r_chiral_restr 0.172 r_nbtor_refined 0.169 r_metal_ion_refined 0.126 r_symmetry_xyhbond_nbd_other 0.098 r_symmetry_nbtor_other 0.096 r_bond_refined_d 0.016 r_gen_planes_refined 0.015 r_gen_planes_other 0.015 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11665 Nucleic Acid Atoms Solvent Atoms 950 Heterogen Atoms 1050
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing