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Hen egg-white lysozyme (HEWL) structure from EuXFEL FXE, multi-hit Droplet-on-Demand (DoD) injection, 9.3 keV photon energy, space group P432121
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6H0K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 3.5 298 1:2 lysozyme (100 mg mL-1 in 50 mM NaOAc (pH 3.5)) and crystallization solution (0.1 M NaOAc (pH 3.5), 5% PEG6000 (v/v), 3.2 M NaCl) at 298K.
Crystal Properties Matthews coefficient Solvent content 2.11 41.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.47 α = 90 b = 79.47 β = 90 c = 38.32 γ = 90
Symmetry Space Group P 43 21 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 STFC Large Pixel Detector 2022-11-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER EUROPEAN XFEL BEAMLINE FXE 1.333 European XFEL FXE
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 1 Droplet on Demand injection
Measurement Diffraction ID Pulse Duration Pulse Repetition Rate Focal Spot Size Pulse Energy Photons Per Pulse 1 50 (fs) 47000 10 9290 (KeV)
Data Reduction Diffraction ID Frames Indexed Crystal Hits Frames Indexed Latices Merged 1 74048 74048
Injection Diffraction ID Description Flow Rate Injector Diameter Injection Power Injector Nozzle Filter Size Carrier Solvent 1 Droplet on Demand Multi Hit undefined (µl/min) undefined (µm) piezoelectric 20 PEG
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 1.38 18.73 100 0.99 0.0836 6.77 479 12383860 35.6
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 1.38 1.4 100 0.01 0.5488 0.9 43
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.38 18.73 1.33 25781 2639 99.96 0.1535 0.1484 0.1486 0.1998 0.2002
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 9.206 f_angle_d 0.948 f_chiral_restr 0.078 f_bond_d 0.009 f_plane_restr 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 996 Nucleic Acid Atoms Solvent Atoms 78 Heterogen Atoms 29
Software Software Software Name Purpose PHENIX refinement CrystFEL data reduction CrystFEL data scaling PHENIX phasing