Navigation Tabs Laser Off Temperature-Jump XFEL structure of Lysozyme Bound to N,N'-diacetylchitobiose
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IEE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 3 291 Lysozyme-inhibitor complex [20 mg/ml lysozyme plus 10 mg/ml N,N'-diacetylchitobiose dissolved in 0.1 M sodium acetate at pH 3.0] mixed with precipitant [28% (w/v) NaCl, 8% (w/v) PEG6000 and 0.1 M sodium acetate at pH 3.0] in a 1:1 ratio
Crystal Properties Matthews coefficient Solvent content 1.93 36.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.061 α = 90 b = 77.061 β = 90 c = 37.223 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 291 CCD MPCCD 2018-07-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER SACLA BEAMLINE BL3 1.2471 SACLA BL3
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 1 injection
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 1.51 30.74 99.98 0.999 18.535 556.53 10094940 14.89
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.51 1.54 0.893
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 1iee 1.51 30.74 1.37 18138 930 99.99 0.1374 0.1357 0.14 0.1679 0.17 19.58
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 12.4253 f_angle_d 1.2401 f_chiral_restr 0.0718 f_bond_d 0.0177 f_plane_restr 0.0115
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1001 Nucleic Acid Atoms Solvent Atoms 91 Heterogen Atoms 36
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction cctbx.xfel data reduction cxi.merge data scaling PHASER phasing
