7DFK

Crystal structure of xylitol-bound glucose isomerase by serial millisecond crystallography


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7CK0 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE7293.5Tris-HCl, Ammonium sulfate, Magnesium sulfate
Crystal Properties
Matthews coefficientSolvent content
2.856.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 94.138α = 90
b = 99.936β = 90
c = 103.156γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298.15PIXELDECTRIS PILATUS 6M2019-11-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPAL/PLS BEAMLINE 11C0.97942PAL/PLS11C

Serial Crystallography

Sample delivery method
Diffraction IDDescriptionSample Delivery Method
1fixed target
Fixed Target
Diffraction IDDescriptionSample HoldingSupport BaseMotion controlSample Solvent
1nylon meshgoniometer

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
11.472.41000.9524.15277.995564
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)
11.41.450.5968

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 REPLACEMENTTHROUGHOUT7CK01.471.781.3395221128799.640.23520.2350.250521.0188
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]
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3033
Nucleic Acid Atoms
Solvent Atoms314
Heterogen Atoms23

Software

Software
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
CrystFELdata reduction
CrystFELdata scaling
PHENIXphasing