9FKC | pdb_00009fkc

Crystal structure of human Glucose-6-phosphate isomerase with citraconate ligand


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7295Protein buffer: 20 mM Tris pH 7.4, 30 mM NaCl, 20 mM citraconate ligand. Reservoir: 21% w/v PEG3500, 0.16 M CaCl2, and 0.058 M HEPES, pH 7.0 Co-crystallization with ligand: Hanging drop: 1.5:0.5:1.5 ul - Protein (8 mg/ml):Seed stock:Reservoir. Cryoprotectant = a mixture containing the mother liquor, 24% v/v glycerol, and 15-20 mM ligand.
Crystal Properties
Matthews coefficientSolvent content
2.3447.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.723α = 90
b = 107.838β = 90
c = 271.481γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2023-12-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX IV BEAMLINE BioMAX0.987MAX IVBioMAX

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim 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
11.646.3299.670.17690.18730.060940.9988.669.131052321.02
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.65799.13.6083.8161.2320.4640.939.2

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)Mean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1.646.321.333101361557199.670.19930.19790.20910.22720.236429.96
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_d9.6813
f_angle_d0.7715
f_chiral_restr0.0482
f_plane_restr0.0088
f_bond_d0.0061
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms17734
Nucleic Acid Atoms
Solvent Atoms1745
Heterogen Atoms105

Software

Software
Software NamePurpose
REFMACrefinement
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing