Navigation Tabs Atomic resolution (1.05 A) XFEL structure of chemically-reduced 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 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 2.69 54.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.99 α = 90 b = 106.99 β = 90 c = 106.99 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 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 1.05 17 99.9 0.89 0.228 3.8 20 218286 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 1.05 1.06 0.262 0.841 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 1.05 16.921 188669 9534 99.962 0.16 0.1591 0.1591 0.1783 0.1781 14.32
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 20.012 r_dihedral_angle_6_deg 16.983 r_lrange_other 15.81 r_dihedral_angle_3_deg 11.317 r_dihedral_angle_2_deg 10.884 r_dihedral_angle_1_deg 7.725 r_scangle_it 7.356 r_scangle_other 7.354 r_mcangle_other 5.826 r_mcangle_it 5.825
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 20.012 r_dihedral_angle_6_deg 16.983 r_lrange_other 15.81 r_dihedral_angle_3_deg 11.317 r_dihedral_angle_2_deg 10.884 r_dihedral_angle_1_deg 7.725 r_scangle_it 7.356 r_scangle_other 7.354 r_mcangle_other 5.826 r_mcangle_it 5.825 r_scbond_it 5.58 r_scbond_other 5.579 r_rigid_bond_restr 5.124 r_mcbond_it 4.393 r_mcbond_other 4.376 r_angle_refined_deg 1.933 r_angle_other_deg 0.681 r_symmetry_xyhbond_nbd_refined 0.25 r_xyhbond_nbd_refined 0.223 r_nbd_refined 0.21 r_symmetry_nbd_refined 0.194 r_symmetry_nbd_other 0.185 r_nbtor_refined 0.181 r_nbd_other 0.157 r_metal_ion_refined 0.123 r_chiral_restr 0.11 r_symmetry_nbtor_other 0.088 r_symmetry_metal_ion_refined 0.081 r_bond_refined_d 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 2553 Nucleic Acid Atoms Solvent Atoms 404 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement CrystFEL data reduction CrystFEL data scaling PHASES phasing
