2GC1

The crystal structure of phosphoglucose isomerase from Pyrococcus furiosus in complex with sorbitol 6-phosphate and zinc


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1X8EPDB ENTRY 1X8E

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.62900.05 M ammonium sulphate, 0.1 M sodium acetate pH 4.6, 20% PEG monoethyl ether 2000, 5 mM D-sorbitol 6-phosphate, 5mM ZnCl2, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
2.5150.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.311α = 90
b = 72.857β = 103.57
c = 71.64γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHOsmic Varimax2005-03-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (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
11.9569.67392.10.0620.0629.64.6283802838025.9
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.952.0688.288.50.3790.37924.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1X8E1.9519.922834628346143691.750.2010.2010.1980.255RANDOM25.979
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]
0.010.090.010.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.661
r_dihedral_angle_4_deg15.698
r_dihedral_angle_3_deg15.424
r_dihedral_angle_1_deg6.342
r_scangle_it2.23
r_angle_refined_deg1.653
r_scbond_it1.455
r_mcangle_it1.102
r_mcbond_it0.65
r_nbtor_refined0.309
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.661
r_dihedral_angle_4_deg15.698
r_dihedral_angle_3_deg15.424
r_dihedral_angle_1_deg6.342
r_scangle_it2.23
r_angle_refined_deg1.653
r_scbond_it1.455
r_mcangle_it1.102
r_mcbond_it0.65
r_nbtor_refined0.309
r_symmetry_vdw_refined0.203
r_nbd_refined0.187
r_xyhbond_nbd_refined0.127
r_symmetry_hbond_refined0.126
r_metal_ion_refined0.117
r_symmetry_metal_ion_refined0.106
r_chiral_restr0.085
r_bond_refined_d0.01
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3027
Nucleic Acid Atoms
Solvent Atoms307
Heterogen Atoms35

Software

Software
Software NamePurpose
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
CCP4data scaling