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Oxidised copper nitrite reductase from Achromobacter cycloclastes determined by serial femtosecond rotation crystallography
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5AKR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 293.15 1.2 M ammonium sulphate, 100 mM citrate buffer, pH 5.0
Crystal Properties Matthews coefficient Solvent content 1.96 37.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.95 α = 90 b = 94.95 β = 90 c = 94.95 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 MX225-HS 2017-10-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER SACLA BEAMLINE BL2 1.242 SACLA BL2
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 1 fixed target
Fixed Target Diffraction ID Description Sample Holding Support Base Motion control Details Sample Solvent 1 Mouted Hampton Cryo Loops 0.7 - 1.0 mm (HR4-965) Mouted Hampton Cryo Loops 0.7 - 1.0 mm (HR4-965) SACLA goniometer 3.4 M ammonium sulfate and 100 mM citrate buffer, pH 5.0
Measurement Diffraction ID Pulse Duration Pulse Repetition Rate Focal Spot Size Pulse Energy Photons Per Pulse 1 10 (fs) 30 437.7 (KeV) 5.7
Data Reduction Diffraction ID Frames Indexed Crystal Hits Frames Indexed Latices Merged 1 1377 1867 1377
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.5 54.88 100 0.115 6.3 220.9 45883 23
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Split (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.54 100 0.904 2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION THROUGHOUT 5AKR 1.5 54.88 43551 2297 100 0.14595 0.1443 0.17695 0.2069 RANDOM 19.41
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_dihedral_angle_2_deg 33.601 r_dihedral_angle_4_deg 20.83 r_dihedral_angle_3_deg 12.837 r_dihedral_angle_1_deg 8.264 r_long_range_B_refined 4.608 r_long_range_B_other 4.283 r_scangle_other 3.365 r_scbond_it 2.454 r_scbond_other 2.329 r_mcangle_it 2.041
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.601 r_dihedral_angle_4_deg 20.83 r_dihedral_angle_3_deg 12.837 r_dihedral_angle_1_deg 8.264 r_long_range_B_refined 4.608 r_long_range_B_other 4.283 r_scangle_other 3.365 r_scbond_it 2.454 r_scbond_other 2.329 r_mcangle_it 2.041 r_mcangle_other 2.041 r_angle_refined_deg 1.612 r_mcbond_it 1.424 r_mcbond_other 1.393 r_angle_other_deg 1.057 r_chiral_restr 0.087 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2574 Nucleic Acid Atoms Solvent Atoms 401 Heterogen Atoms 37
Software Software Software Name Purpose CrystFEL data reduction REFMAC refinement