Navigation Tabs XFEL Serial Crystallography Reveals the Room Temperature Structure of Methyl-Coenzyme M Reductase
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3M1V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.55 300 18% PEG 400, 150mM Mg Acetate, 100mM HEPES (pH 7.5)
Crystal Properties Matthews coefficient Solvent content 2.23 44.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.082 α = 90 b = 119.777 β = 91.73 c = 123.21 γ = 90
Symmetry Space Group P 1 21 1
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 2020-07-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER SLAC LCLS BEAMLINE MFX 1.3007 SLAC LCLS MFX
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 1 Drop On Tape injection
Measurement Diffraction ID Pulse Duration Pulse Repetition Rate Focal Spot Size Pulse Energy Photons Per Pulse 1 30 (fs) 30 16 9.5 (KeV)
Data Reduction Diffraction ID Frames Indexed Crystal Hits Frames Indexed Latices Merged 1 24589
Injection Diffraction ID Description Flow Rate Injector Diameter Injection Power Injector Nozzle Filter Size Carrier Solvent 1 Crystal slurry is injected onto a kapton tape from an acoustic droplet injector (ADE). The drop travels on the tape towards the X-ray interaction point where it is hit by the XFEL beam. This is the Drop-On-Tape (DOT) sample delivery system used by our team previously. undefined (µl/min) undefined (µm) 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 1.9 21.25 99.91 0.979 0.515 3.356 41.43 189345 26.7
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 1.9 1.93 99.82 0.379 0.831 0.696 9.89
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 R-Free Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3M1V 1.9 21.25 1.34 188906 2008 99.84 0.1528 0.1524 0.1863 30.52
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 f_dihedral_angle_d 6.3826 f_angle_d 0.8169 f_chiral_restr 0.0464 f_plane_restr 0.0069 f_bond_d 0.0044
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19098 Nucleic Acid Atoms Solvent Atoms 734 Heterogen Atoms 195
Software Software Software Name Purpose PHENIX refinement cctbx.xfel data reduction cxi.merge data scaling Coot model building PHASER phasing
