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1.8 A resolution room temperature structure of Thermolysin recorded using an XFEL
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2TLI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 298 300 ul of the protein stock was mixed in a 1:1 ratio with 40% PEG 2000, 100 mM MES pH 6.5, 5 mM CaCl2. Crystallization occurred within minutes.
Crystal Properties Matthews coefficient Solvent content 2.39 48.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.0407 α = 90 b = 93.0407 β = 90 c = 130.41 γ = 120
Symmetry Space Group P 61 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 298 PIXEL CS-PAD detector Collected at the CXI instrument at LCLS/SLAC using the CSPAD 2013-03-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER SLAC LCLS BEAMLINE CXI 1.27 SLAC LCLS CXI
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 1.8 34.27 100 71.7 1468 31458 16.3967395539
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 1.8 1.86 100 14.6
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 2tli 1.8 34.27 1.42149651097 58500 3063 99.9128964492 0.212950766366 0.211866857775 0.2159 0.232602531993 0.2336 20.1244048785
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 12.5608297587 f_angle_d 0.923727439628 f_chiral_restr 0.0342922692207 f_bond_d 0.00514226974771 f_plane_restr 0.0040116139072
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2415 Nucleic Acid Atoms Solvent Atoms 324 Heterogen Atoms 5
Software Software Software Name Purpose PHENIX refinement cctbx.xfel data reduction