1QXR

Crystal structure of phosphoglucose isomerase from Pyrococcus furiosus in complex with 5-phosphoarabinonate


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.629525% PEG 4000, 0.2M ammonium acetate, 0.1M 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 IVmirrors2003-07-04MSINGLE 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
11.736.892.50.04112.52.73827923.6
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)
1.71.7688.20.2973.32.73618

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 DIFFRACTIONREFINEMENTTHROUGHOUT1QXJ1.71538161194092.30.2230.2230.2210.264RANDOM29.621
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]
1.16-0.72-0.46-0.231.61-1.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg19.894
r_dihedral_angle_1_deg4.728
r_scangle_it3.617
r_scbond_it2.27
r_angle_refined_deg1.54
r_mcangle_it1.487
r_mcbond_it0.84
r_nbd_refined0.218
r_symmetry_hbond_refined0.158
r_symmetry_vdw_refined0.156
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg19.894
r_dihedral_angle_1_deg4.728
r_scangle_it3.617
r_scbond_it2.27
r_angle_refined_deg1.54
r_mcangle_it1.487
r_mcbond_it0.84
r_nbd_refined0.218
r_symmetry_hbond_refined0.158
r_symmetry_vdw_refined0.156
r_xyhbond_nbd_refined0.142
r_chiral_restr0.107
r_bond_refined_d0.013
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3004
Nucleic Acid Atoms
Solvent Atoms126
Heterogen Atoms32

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata reduction
CrystalCleardata scaling