6S1D

Structure of thaumatin determined at SwissFEL using native-SAD at 4.57 keV from 20,000 diffraction patterns


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE72931.6 M potassium sodium tartrate tetrahydrate, 100 mM Na-HEPES
Crystal Properties
Matthews coefficientSolvent content
2.9157.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.5α = 90
b = 58.5β = 90
c = 151.25γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray297PIXELPSI JUNGFRAU 1MKB2018-08-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1FREE ELECTRON LASERSwissFEL ARAMIS BEAMLINE ESA2.713SwissFEL ARAMISESA

Serial Crystallography

Sample delivery method
Diffraction IDDescriptionSample Delivery Method
1injection

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
12.6535.7110011.1412514552
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.652.71

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONSADFREE R-VALUE2.6531.9791.331455272899.980.15520.15290.1962
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_d7.809
f_angle_d0.931
f_chiral_restr0.058
f_bond_d0.008
f_plane_restr0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1550
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms10

Software

Software
Software NamePurpose
PHENIXrefinement
CrystFELdata reduction
CrystFELdata scaling
CRANK2phasing