8CWE

20ns Temperature-Jump (Dark2) XFEL structure of Lysozyme Bound to N,N'-diacetylchitobiose


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1IEE 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE3291Lysozyme-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 coefficientSolvent content
1.9336.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.061α = 90
b = 77.061β = 90
c = 37.223γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray291CCDMPCCD2018-07-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1FREE ELECTRON LASERSACLA BEAMLINE BL31.2468SACLABL3

Serial Crystallography

Sample delivery method
Diffraction IDDescriptionSample Delivery Method
1injection

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.4830.7499.980.99411.287162.5312734815.32
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.481.510.823

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1iee1.4830.741.36192459841000.13080.12910.162419.57
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
KeyRefinement Restraint Deviation
f_dihedral_angle_d12.5397
f_angle_d1.2645
f_chiral_restr0.084
f_bond_d0.019
f_plane_restr0.0114
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1001
Nucleic Acid Atoms
Solvent Atoms95
Heterogen Atoms36

Software

Software
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
cctbx.xfeldata reduction
cxi.mergedata scaling
PHASERphasing