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Crystal structure of two-domain Cu nitrite reductase from Bradyrhizobium sp. ORS 375
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5I6K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 298 1.2 M ammonium sulfate,
0.05 M MES pH6.0
Crystal Properties Matthews coefficient Solvent content 2.68 54.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.929 α = 90 b = 106.929 β = 90 c = 106.929 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 PIXEL DECTRIS PILATUS 6M-F 2018-06-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9159 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.47 106.93 100 0.081 0.088 0.034 0.998 11.3 6.5 69285 14.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.47 1.5 100 1.018 1.105 0.428 0.638 1.5 6.6
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5I6K 1.47 50.93 65827 3384 99.96 0.1417 0.1408 0.1571 0.1652 RANDOM 20.518
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 37.046 r_dihedral_angle_4_deg 21.128 r_dihedral_angle_3_deg 11.495 r_dihedral_angle_1_deg 7.237 r_angle_refined_deg 1.667 r_angle_other_deg 0.984 r_chiral_restr 0.1 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.046 r_dihedral_angle_4_deg 21.128 r_dihedral_angle_3_deg 11.495 r_dihedral_angle_1_deg 7.237 r_angle_refined_deg 1.667 r_angle_other_deg 0.984 r_chiral_restr 0.1 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2617 Nucleic Acid Atoms Solvent Atoms 520 Heterogen Atoms 66
Software Software Software Name Purpose DIALS data reduction MOLREP phasing ARP/wARP model building Coot model building REFMAC refinement PDB_EXTRACT data extraction