8CW0

20us Temperature-Jump (Light) XFEL structure of Lysozyme


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE3291Lysozyme [20 mg/ml 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
2.1141.65

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.519α = 90
b = 79.519β = 90
c = 38.212γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray291CCDMPCCD2017-11-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1FREE ELECTRON LASERSACLA BEAMLINE BL31.24SACLABL3

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
11.5728.1199.970.99210.844125.46220828715.49
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)
11.571.60.445

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-VALUE1iee1.5728.111.991767089999.990.1460.14490.166820.29
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_d13.0272
f_angle_d0.9111
f_chiral_restr0.0593
f_bond_d0.0104
f_plane_restr0.0086
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1001
Nucleic Acid Atoms
Solvent Atoms90
Heterogen Atoms14

Software

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