6IRK

Crystal structure of glucose isomerase by fixed-target serial femtosecond crystallography


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5Y4J 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE7293.5Tris-HCl, Ammonium sulfate, Magnesium sulfate
Crystal Properties
Matthews coefficientSolvent content
2.7354.89

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 93.05α = 90
b = 99β = 90
c = 101.92γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray296CCDRAYONIX MX225-HSKB mirror2018-10-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1FREE ELECTRON LASERPAL-XFEL BEAMLINE CSI1.2782PAL-XFELCSI

Serial Crystallography

Sample delivery method
Diffraction IDDescriptionSample Delivery Method
1fixed targetfixed target
Fixed Target
Diffraction IDDescriptionSample HoldingSupport BaseMotion controlSample Solvent
110000mesh
Measurement
Diffraction IDPulse DurationPulse Repetition RateFocal Spot SizePulse EnergyPhotons Per Pulse
1203049700
Data Reduction
Diffraction IDFrames IndexedCrystal HitsTotal Frames
129157134325

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)R Split (All)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
11.7571.941000.92840.21634.03356.847861
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)R Split (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.751.811000.7960.64711.45125.2

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 REPLACEMENTTHROUGHOUT5Y4J1.7571.0131.3447666198899.80.18270.18180.203
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_d9.762
f_angle_d1.078
f_chiral_restr0.054
f_bond_d0.01
f_plane_restr0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3038
Nucleic Acid Atoms
Solvent Atoms209
Heterogen Atoms2

Software

Software
Software NamePurpose
PHENIXrefinement
PHASERphasing
PDB_EXTRACTdata extraction
CrystFELdata reduction
CrystFELdata scaling