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XFEL structure of Class Ib ribonucleotide reductase dimanganese(II) NrdF in complex with oxidized NrdI from Bacillus cereus
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4BMO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 5 293 0.1 M MnCl2, 0.1 M sodium acetate 5.0, 5% PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.82 56.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.438 α = 90 b = 125.634 β = 90 c = 144.997 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 300 CCD RAYONIX MX340-HS 2018-12-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER SLAC LCLS BEAMLINE MFX 1.300734 SLAC LCLS MFX
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 1 drop on tape combined with acoustic droplet ejection injection
Measurement Diffraction ID Pulse Duration Pulse Repetition Rate Focal Spot Size Pulse Energy Photons Per Pulse 1 35 (fs) 30 9.5 (KeV)
Data Reduction Diffraction ID Frames Indexed Crystal Hits Frames Indexed Latices Merged 1
Injection Diffraction ID Description Flow Rate Injector Diameter Injection Power Injector Nozzle Filter Size Carrier Solvent 1 acoustic droplet injection 8 (µl/min) undefined (µm) focused acoustic pulse mother liquor
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 2 51.59 99.91 0.989 0.111 3.247 66.94 38319 35.45
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 2 2.034 100 0.32 0.863 0.654 25.42
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4bmo 2 24.17 1.34 38253 1909 99.91 0.1609 0.1591 0.16 0.1956 0.1958 47.4506
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3355 Nucleic Acid Atoms Solvent Atoms 159 Heterogen Atoms 34
Software Software Software Name Purpose PHENIX refinement cctbx.xfel data reduction PHASER phasing cctbx.xfel.merge data scaling