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Reduced copper nitrite reductase from Achromobacter cycloclastes determined by serial femtosecond rotation crystallography
Serial Crystallography (SX)
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 1.94 36.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.61 α = 90 b = 94.61 β = 90 c = 94.61 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 Mounted Hampton Cryo Loops 0.7 - 1.0 mm (HR4-965) Mounted Hampton Cryo Loops 0.7 - 1.0 mm (HR4-965) SACLA goniometer 3.4 M Na-malonate, pH 5.0 and 100 mM NaNO2.
Measurement Diffraction ID Pulse Duration Pulse Repetition Rate Focal Spot Size Pulse Energy Photons Per Pulse 1 10 (fs) 30 437.7 (KeV)
Data Reduction Diffraction ID Frames Indexed Crystal Hits Frames Indexed Latices Merged 1 410 581 410
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 1.6 54.62 100 0.158 5.4 66.1 37489 24.9
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 1.6 1.64 100 0.708 2.7 44.3
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION THROUGHOUT 1.6 54.68 35562 1883 99.98 0.16823 0.16658 0.1991 0.2268 RANDOM 21.872
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 34.255 r_dihedral_angle_1_deg 21.462 r_dihedral_angle_4_deg 20.098 r_dihedral_angle_3_deg 12.667 r_long_range_B_refined 4.889 r_long_range_B_other 4.722 r_scangle_other 3.726 r_scbond_it 2.471 r_scbond_other 2.465 r_mcangle_other 2.283
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.255 r_dihedral_angle_1_deg 21.462 r_dihedral_angle_4_deg 20.098 r_dihedral_angle_3_deg 12.667 r_long_range_B_refined 4.889 r_long_range_B_other 4.722 r_scangle_other 3.726 r_scbond_it 2.471 r_scbond_other 2.465 r_mcangle_other 2.283 r_mcangle_it 2.277 r_mcbond_it 1.593 r_mcbond_other 1.58 r_angle_refined_deg 1.533 r_angle_other_deg 1.009 r_chiral_restr 0.07 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 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 257 Heterogen Atoms 58
Software Software Software Name Purpose REFMAC refinement CrystFEL data reduction