1QXJ

Crystal structure of native phosphoglucose isomerase from Pyrococcus furiosus


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1PLZPDB ENTRY 1PLZ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.629525% PEG 4000, 0.2M ammonium acetate, 0.1 M sodium acetate pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.345

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 36α = 73.7
b = 39.7β = 78.5
c = 74.7γ = 72.6
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IVmirrors2002-07-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH3R1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.836.792.10.06518.53.743484520.6
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.81.8683.40.3242.73.83464

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 1PLZ1.81534789166194.190.19710.19710.194340.24863RANDOM25.085
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]
1.34-0.78-0.28-0.11.51-1.51
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg19.282
r_dihedral_angle_1_deg4.605
r_scangle_it3.475
r_scbond_it2.102
r_angle_refined_deg1.472
r_mcangle_it1.338
r_mcbond_it0.726
r_nbd_refined0.213
r_symmetry_vdw_refined0.177
r_symmetry_hbond_refined0.172
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg19.282
r_dihedral_angle_1_deg4.605
r_scangle_it3.475
r_scbond_it2.102
r_angle_refined_deg1.472
r_mcangle_it1.338
r_mcbond_it0.726
r_nbd_refined0.213
r_symmetry_vdw_refined0.177
r_symmetry_hbond_refined0.172
r_xyhbond_nbd_refined0.142
r_chiral_restr0.108
r_bond_refined_d0.011
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3004
Nucleic Acid Atoms
Solvent Atoms249
Heterogen Atoms2

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata reduction
CrystalCleardata scaling
MOLREPphasing