Navigation Tabs Atomic resolution (1.15 A) XFEL structure of as-isolated copper nitrite reductase from Bradyrhizobium sp. at low pH (5.5) 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 6ZAS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 1.8 M ammonium sulphate, 50 mM HEPES (pH 5.0)
Crystal Properties Matthews coefficient Solvent content 2.71 54.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.32 α = 90 b = 107.32 β = 90 c = 107.32 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 2021-07-06 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 1.1 17 99.8 0.975 0.122 6.5 20 165516 10.5
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 1.11 0.225 0.964 1.4
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.15 17 145252 7345 99.956 0.151 0.1499 0.1517 0.1739 0.1744 18.457
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 18.298 r_lrange_other 18.298 r_dihedral_angle_6_deg 16.913 r_dihedral_angle_3_deg 13.759 r_scangle_it 10.671 r_scangle_other 10.357 r_dihedral_angle_2_deg 9.442 r_scbond_it 8.138 r_scbond_other 7.861 r_dihedral_angle_1_deg 7.709
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 18.298 r_lrange_other 18.298 r_dihedral_angle_6_deg 16.913 r_dihedral_angle_3_deg 13.759 r_scangle_it 10.671 r_scangle_other 10.357 r_dihedral_angle_2_deg 9.442 r_scbond_it 8.138 r_scbond_other 7.861 r_dihedral_angle_1_deg 7.709 r_mcangle_other 7.591 r_mcangle_it 7.582 r_rigid_bond_restr 5.841 r_mcbond_it 5.778 r_mcbond_other 5.763 r_angle_refined_deg 1.951 r_angle_other_deg 0.708 r_symmetry_xyhbond_nbd_refined 0.451 r_symmetry_nbd_refined 0.424 r_nbd_refined 0.259 r_xyhbond_nbd_refined 0.257 r_symmetry_nbd_other 0.204 r_nbtor_refined 0.181 r_nbd_other 0.169 r_metal_ion_refined 0.144 r_chiral_restr 0.12 r_xyhbond_nbd_other 0.116 r_symmetry_nbtor_other 0.089 r_bond_refined_d 0.016 r_symmetry_metal_ion_refined 0.014 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2662 Nucleic Acid Atoms Solvent Atoms 421 Heterogen Atoms 94
Software Software Software Name Purpose SHELXL refinement CrystFEL data reduction CrystFEL data scaling PHASES phasing
