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Recombinant Sperm Whale P6 Myoglobin Solved with Single Pulse Free Electron Laser Data
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VXA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9 295 2.2 - 2.8M (NH4)2SO4 in 20mM TrisHCl
Crystal Properties Matthews coefficient Solvent content 3.06 59.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.309 α = 90 b = 90.309 β = 90 c = 45.204 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL CS-PAD CXI-1 2012-12-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER SLAC LCLS BEAMLINE XPP 1.31 SLAC LCLS XPP
Serial Crystallography Fixed Target Diffraction ID Description Sample Holding Support Base Motion control Details Sample Solvent 1 polycarbonate grid goniometer DCSS 8% NaCl, 0.1M Sodium Acetage pH 4.0, 100mM Gadoteridol
Measurement Diffraction ID Pulse Duration Pulse Repetition Rate Focal Spot Size Pulse Energy Photons Per Pulse 1 30 (fs) 50 9.5 (KeV) 1
Data Reduction Diffraction ID Frames Indexed Crystal Hits Frames Indexed Latices Merged 1 739 932 739
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.36 39.15 95.7 33.94 25.1 43767 15.24
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.36 1.37 52 52 1.57
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 FREE R-VALUE 1VXA 1.36 39.105 2.15 43729 2585 95.6 0.1603 0.1586 0.1608 0.1881 0.1922 20.7716
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 15.506 f_angle_d 1.432 f_chiral_restr 0.087 f_bond_d 0.013 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1222 Nucleic Acid Atoms Solvent Atoms 364 Heterogen Atoms 113
Software Software Software Name Purpose cctbx.xfel data reduction MOLREP phasing PDB_EXTRACT data extraction PHENIX refinement