Navigation Tabs Atomic resolution (1.00 A) XFEL structure of as-isolated copper nitrite reductase from Bradyrhizobium sp. at high pH (7.3) determined by serial femtosecond rotation crystallography (SF-ROX) at 100 K
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8S0W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 1.8 M ammonium sulphate, 100 mM Tris (pH 7.3)
Crystal Properties Matthews coefficient Solvent content 2.71 54.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.82 α = 90 b = 103.82 β = 90 c = 64.47 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 293 CCD RAYONIX MX300-HS 2022-06-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER SACLA BEAMLINE BL2 0.954 SACLA BL2
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 1 Single crystal (SF-ROX) fixed target
Fixed Target Diffraction ID Description Sample Holding Support Base Motion control Details Sample Solvent 1 Single crystal (SF-ROX)
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 17 100 0.935 0.16 6.1 20 212579 8.8
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 1.01 0.202 1.054 1.2
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1 16.765 212404 10781 99.932 0.136 0.1347 0.1348 0.1566 0.1565 RANDOM
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_lrange_it 19.475 r_lrange_other 16.745 r_dihedral_angle_2_deg 16.058 r_dihedral_angle_6_deg 16.022 r_dihedral_angle_3_deg 12.312 r_mcangle_other 11.049 r_mcangle_it 11.039 r_scangle_it 10.662 r_scangle_other 10.566 r_mcbond_it 9.129
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 19.475 r_lrange_other 16.745 r_dihedral_angle_2_deg 16.058 r_dihedral_angle_6_deg 16.022 r_dihedral_angle_3_deg 12.312 r_mcangle_other 11.049 r_mcangle_it 11.039 r_scangle_it 10.662 r_scangle_other 10.566 r_mcbond_it 9.129 r_mcbond_other 9.125 r_scbond_it 8.135 r_scbond_other 8.054 r_dihedral_angle_1_deg 7.972 r_rigid_bond_restr 7.349 r_angle_refined_deg 1.898 r_angle_other_deg 0.69 r_symmetry_xyhbond_nbd_refined 0.25 r_nbd_refined 0.229 r_xyhbond_nbd_refined 0.223 r_symmetry_nbd_refined 0.191 r_symmetry_nbd_other 0.19 r_nbd_other 0.19 r_nbtor_refined 0.178 r_metal_ion_refined 0.144 r_chiral_restr 0.113 r_symmetry_nbtor_other 0.088 r_symmetry_metal_ion_refined 0.035 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2554 Nucleic Acid Atoms Solvent Atoms 484 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement CrystFEL data reduction CrystFEL data scaling PHASES phasing
