☰ Navigation Tabs
Nitrite-bound copper nitrite reductase from Bradyrhizobium sp. ORS 375 (two-domain) at low dose (0.5 MGy)
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 5.5 297 1.6 M (NH4)2SO4 and 50mM HEPES buffer pH5.5
Crystal Properties Matthews coefficient Solvent content 2.72 54.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.566 α = 90 b = 107.566 β = 90 c = 107.566 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 EIGER X 16M 2020-02-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 0.8000 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.48 48.15 99.9 0.094 0.039 0.999 10.8 6.9 65671
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.48 1.5 98 1.638 0.667 0.541 1.1
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 1.48 48.15 65659 3481 99.91 0.1481 0.1467 0.1468 0.1762 0.1776 RANDOM 21.131
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 33.623 r_dihedral_angle_4_deg 21.654 r_dihedral_angle_3_deg 14.213 r_dihedral_angle_1_deg 8.042 r_angle_refined_deg 1.954 r_angle_other_deg 1.458 r_chiral_restr 0.095 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.623 r_dihedral_angle_4_deg 21.654 r_dihedral_angle_3_deg 14.213 r_dihedral_angle_1_deg 8.042 r_angle_refined_deg 1.954 r_angle_other_deg 1.458 r_chiral_restr 0.095 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2666 Nucleic Acid Atoms Solvent Atoms 532 Heterogen Atoms 124
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing