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Damage-free nitrite-bound copper nitrite reductase from Bradyrhizobium sp. ORS 375 (two-domain) determined by serial femtosecond rotation crystallography
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6THF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 291 1.6/1.8 M (NH4)2SO4 and 50mM HEPES buffer pH 5/ pH 5.5
Crystal Properties Matthews coefficient Solvent content 2.6 56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.95 α = 90 b = 106.95 β = 90 c = 106.95 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 RAYONIX MX300-HS 2020-02-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER SACLA BEAMLINE BL2 1.2398 SACLA BL2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) R Split (All) 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 1.3 75.63 99.9 0.951 0.163 4.1 73.4 99872 16.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) R Split (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.3 1.35 99.5 0.016 1.126 1.4
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 6THF 1.3 29.8 99687 5033 99.9 0.1583 0.1558 0.1615 0.2061 0.2106 RANDOM 22.613
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 35.631 r_dihedral_angle_4_deg 20.814 r_dihedral_angle_3_deg 13.402 r_dihedral_angle_1_deg 8.361 r_rigid_bond_restr 3.333 r_angle_refined_deg 1.903 r_angle_other_deg 1.514 r_chiral_restr 0.104 r_bond_refined_d 0.015 r_gen_planes_refined 0.012
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.631 r_dihedral_angle_4_deg 20.814 r_dihedral_angle_3_deg 13.402 r_dihedral_angle_1_deg 8.361 r_rigid_bond_restr 3.333 r_angle_refined_deg 1.903 r_angle_other_deg 1.514 r_chiral_restr 0.104 r_bond_refined_d 0.015 r_gen_planes_refined 0.012 r_gen_planes_other 0.004 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2662 Nucleic Acid Atoms Solvent Atoms 459 Heterogen Atoms 103
Software Software Software Name Purpose REFMAC refinement CrystFEL data reduction XDS data scaling REFMAC phasing