Navigation Tabs Atomic resolution (1.02 A) XFEL structure of nitrite-bound copper nitrite reductase from Bradyrhizobium sp. 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 8RFL
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 54.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.89 α = 90 b = 103.89 β = 90 c = 64.35 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 99.9 0.935 0.166 5.3 20 212451 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 0.206 0.986 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 1.02 16.765 200220 10169 99.97 0.147 0.1461 0.1463 0.1607 0.161 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 20.383 r_lrange_other 17.259 r_dihedral_angle_6_deg 15.983 r_dihedral_angle_2_deg 13.426 r_dihedral_angle_3_deg 13.16 r_mcangle_it 8.984 r_mcangle_other 8.982 r_dihedral_angle_1_deg 7.829 r_scangle_it 7.009 r_scangle_other 6.867
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 20.383 r_lrange_other 17.259 r_dihedral_angle_6_deg 15.983 r_dihedral_angle_2_deg 13.426 r_dihedral_angle_3_deg 13.16 r_mcangle_it 8.984 r_mcangle_other 8.982 r_dihedral_angle_1_deg 7.829 r_scangle_it 7.009 r_scangle_other 6.867 r_mcbond_it 6.197 r_mcbond_other 6.194 r_scbond_it 4.67 r_scbond_other 4.534 r_rigid_bond_restr 2.968 r_angle_refined_deg 1.615 r_angle_other_deg 0.658 r_symmetry_xyhbond_nbd_other 0.275 r_nbd_refined 0.246 r_xyhbond_nbd_refined 0.226 r_symmetry_nbd_other 0.193 r_symmetry_xyhbond_nbd_refined 0.187 r_nbtor_refined 0.178 r_nbd_other 0.169 r_metal_ion_refined 0.132 r_symmetry_nbd_refined 0.125 r_chiral_restr 0.097 r_symmetry_nbtor_other 0.088 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_symmetry_metal_ion_refined 0.009 r_bond_other_d 0.003 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2554 Nucleic Acid Atoms Solvent Atoms 438 Heterogen Atoms 51
Software Software Software Name Purpose REFMAC refinement CrystFEL data reduction CrystFEL data scaling PHASES phasing
