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As isolated MSOX movie series dataset 5 (2 MGy) of the copper nitrite reductase from Bradyrhizobium sp. ORS 375 (two-domain)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7QXK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 297 1.8 M (NH4)2SO2 and 50mM HEPES buffer pH 5
Crystal Properties Matthews coefficient Solvent content 2.32 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.25 α = 90 b = 107.25 β = 90 c = 107.25 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 4M 2021-04-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B1 0.99999 SPring-8 BL26B1
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 1.35 48.01 98.1 0.036 0.04 0.015 1 25 5.7 88290 11.38
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 1.35 1.37 84.7 0.357 0.452 0.273 0.79 2.6 2.3
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 7QXK 1.35 48.01 83590 4667 98.04 0.12468 0.12366 0.1236 0.14318 0.143 RANDOM 15.511
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 35.611 r_dihedral_angle_4_deg 22.671 r_dihedral_angle_3_deg 11.678 r_dihedral_angle_1_deg 8.127 r_long_range_B_refined 4.993 r_long_range_B_other 4.191 r_scangle_other 3.204 r_scbond_it 2.301 r_scbond_other 2.251 r_mcangle_other 2.196
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.611 r_dihedral_angle_4_deg 22.671 r_dihedral_angle_3_deg 11.678 r_dihedral_angle_1_deg 8.127 r_long_range_B_refined 4.993 r_long_range_B_other 4.191 r_scangle_other 3.204 r_scbond_it 2.301 r_scbond_other 2.251 r_mcangle_other 2.196 r_mcangle_it 2.195 r_angle_refined_deg 2.089 r_angle_other_deg 1.458 r_mcbond_it 1.457 r_mcbond_other 1.447 r_chiral_restr 0.114 r_bond_refined_d 0.017 r_gen_planes_refined 0.012 r_gen_planes_other 0.003 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2614 Nucleic Acid Atoms Solvent Atoms 578 Heterogen Atoms 53
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing