2GC3

The crystal structure of phosphoglucose isomerase from Pyrococcus furiosus in complex with mannose 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, 5mM ZnCl2, 5mM mannose 6-phosphate, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
2.2845.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.346α = 90
b = 74.016β = 90
c = 74.835γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHOsmic Varimax2005-03-29MSINGLE 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
12.174.8351000.1040.1045.96.9234772347722.9
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)
2.12.211001000.3660.36626.63361

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 1X8E2.119.8523440120299.990.1620.1620.1580.235RANDOM25.049
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]
0.01-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.343
r_dihedral_angle_3_deg15.8
r_dihedral_angle_4_deg14.372
r_scangle_it12.173
r_scbond_it9.139
r_mcangle_it7.819
r_mcbond_it6.85
r_dihedral_angle_1_deg6.472
r_angle_refined_deg1.246
r_nbtor_refined0.306
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.343
r_dihedral_angle_3_deg15.8
r_dihedral_angle_4_deg14.372
r_scangle_it12.173
r_scbond_it9.139
r_mcangle_it7.819
r_mcbond_it6.85
r_dihedral_angle_1_deg6.472
r_angle_refined_deg1.246
r_nbtor_refined0.306
r_symmetry_hbond_refined0.232
r_symmetry_vdw_refined0.199
r_nbd_refined0.181
r_xyhbond_nbd_refined0.116
r_chiral_restr0.081
r_metal_ion_refined0.061
r_bond_refined_d0.009
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3020
Nucleic Acid Atoms
Solvent Atoms353
Heterogen Atoms34

Software

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