Navigation Tabs Sub-atomic resolution (0.95 A) XFEL structure of nitrite-bound copper nitrite reductase from Achromobacter cycloclastes 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 6GT0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 1.2 M ammonium sulphate, 50 mM citrate (pH 4.8)
Crystal Properties Matthews coefficient Solvent content 1.97 37.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.32 α = 90 b = 95.32 β = 90 c = 95.32 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 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 0.95 17 99.9 0.853 0.238 4 20 180355 6.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 0.95 0.96 0.235
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 0.95 16.856 180225 9084 99.954 0.147 0.1456 0.1461 0.1724 0.1725 10.273
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 19.089 r_dihedral_angle_6_deg 16.631 r_lrange_other 14.695 r_dihedral_angle_3_deg 11.999 r_dihedral_angle_1_deg 8.398 r_dihedral_angle_2_deg 6.764 r_scangle_it 6.476 r_scangle_other 5.788 r_rigid_bond_restr 5.396 r_scbond_it 4.971
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 19.089 r_dihedral_angle_6_deg 16.631 r_lrange_other 14.695 r_dihedral_angle_3_deg 11.999 r_dihedral_angle_1_deg 8.398 r_dihedral_angle_2_deg 6.764 r_scangle_it 6.476 r_scangle_other 5.788 r_rigid_bond_restr 5.396 r_scbond_it 4.971 r_scbond_other 4.44 r_mcangle_it 3.916 r_mcangle_other 3.916 r_mcbond_it 2.941 r_mcbond_other 2.926 r_angle_refined_deg 2.038 r_angle_other_deg 0.715 r_xyhbond_nbd_other 0.575 r_symmetry_xyhbond_nbd_refined 0.39 r_symmetry_nbd_refined 0.367 r_xyhbond_nbd_refined 0.285 r_nbd_refined 0.252 r_nbd_other 0.244 r_symmetry_nbd_other 0.201 r_nbtor_refined 0.177 r_symmetry_xyhbond_nbd_other 0.169 r_chiral_restr 0.115 r_metal_ion_refined 0.105 r_symmetry_nbtor_other 0.087 r_bond_refined_d 0.015 r_gen_planes_refined 0.011 r_symmetry_metal_ion_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2561 Nucleic Acid Atoms Solvent Atoms 503 Heterogen Atoms 38
Software Software Software Name Purpose SHELXL refinement CrystFEL data reduction CrystFEL data scaling PHASES phasing
