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Hen egg-white lysozyme structure embedded in LCP medium at 95% relative humidity
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3WUN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 SMALL TUBES 3 297 20% NaCl, 6% PEG 6000, 0.1M sodium acetate pH 3.0
Crystal Properties Matthews coefficient Solvent content 2.07 40.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79 α = 90 b = 79 β = 90 c = 38 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 297 PIXEL DECTRIS EIGER X 4M 2024-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.976 PETRA III, EMBL c/o DESY P14 (MX2)
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 1 fixed target chips fixed target
Fixed Target Diffraction ID Description Sample Holding Support Base Motion control Details Sample Solvent 1 HARE chips
Measurement Diffraction ID Pulse Duration Pulse Repetition Rate Focal Spot Size Pulse Energy Photons Per Pulse 1 undefined (fs) undefined (KeV)
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 1.7 55.86 100 0.9638 0.1635 5.22 124.9 13757 21.84
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 1.7 1.76 0.6276 0.6417 1.58
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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 1.7 55.86 13757 653 100 0.1616 0.1598 0.1597 0.1988 0.1987 24.68
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 14.2302 f_angle_d 0.9834 f_chiral_restr 0.0644 f_plane_restr 0.0132 f_bond_d 0.0075
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1001 Nucleic Acid Atoms Solvent Atoms 139 Heterogen Atoms 18
Software Software Software Name Purpose Coot model building PHENIX refinement CrystFEL data reduction CrystFEL data scaling PHASER phasing