6YOE

Structure of Lysozyme from SiN IMISX setup collected by still serial crystallography on crystals prelocated by 2D X-ray phase-contrast imaging


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5D5F 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1LIPIDIC CUBIC PHASE4.52930.5-1 M NaBr, 50-100 mM CH3COONa, pH 4.5, and 15-30 %(v/v) PEG400
Crystal Properties
Matthews coefficientSolvent content
2.1743.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.5α = 90
b = 78.5β = 90
c = 40.46γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2019-12-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1SLSX06SA

Serial Crystallography

Sample delivery method
Diffraction IDDescriptionSample Delivery Method
1fixed target
Fixed Target
Diffraction IDDescriptionSample HoldingSupport BaseMotion controlSample Solvent
1IMISXSiN3D-printed holder in standard goniometer base

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim I (All)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
11.8555.511000.260.992.311.291124746.37
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.851.8996.41.20.220.855.6

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-VALUE5D5F1.8555.511.331124756399.80.26440.26330.284647.06
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_d16.1881
f_angle_d0.4448
f_chiral_restr0.0372
f_plane_restr0.0032
f_bond_d0.0026
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1000
Nucleic Acid Atoms
Solvent Atoms55
Heterogen Atoms21

Software

Software
Software NamePurpose
CrystFELdata scaling
PHENIXrefinement
CrystFELdata reduction
PHENIXphasing