4LTA

The crystal structure of the P132R, Y133G mutant of Pyrococcus furiosus phosphoglucose isomerase in complex with manganese and 5-phospho-D-arabinonate.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1X7NPDB ENTRY 1X7N

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.52900.35M magnesium chloride, 0.1M sodium acetate, 19% PEG4000, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
2.448.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.95α = 90
b = 74.47β = 90
c = 75.9γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MDiamond I032011-05-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.97630DiamondI03

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
12.0426.5899.60.07476.32699426994
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)
12.042.0999.90.2196.41969

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 1X7N2.0426.58269942563513561000.220.221250.217230.29492RANDOM42.791
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]
-0.69-2.433.13
RMS Deviations
KeyRefinement Restraint Deviation
r_scbond_it98.411
r_scangle_it73.77
r_mcbond_it46.146
r_mcangle_it44.184
r_dihedral_angle_2_deg32.896
r_dihedral_angle_4_deg17.472
r_dihedral_angle_3_deg15.413
r_dihedral_angle_1_deg6.479
r_angle_refined_deg1.417
r_chiral_restr0.099
RMS Deviations
KeyRefinement Restraint Deviation
r_scbond_it98.411
r_scangle_it73.77
r_mcbond_it46.146
r_mcangle_it44.184
r_dihedral_angle_2_deg32.896
r_dihedral_angle_4_deg17.472
r_dihedral_angle_3_deg15.413
r_dihedral_angle_1_deg6.479
r_angle_refined_deg1.417
r_chiral_restr0.099
r_bond_refined_d0.013
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3032
Nucleic Acid Atoms
Solvent Atoms140
Heterogen Atoms48

Software

Software
Software NamePurpose
GDAdata collection
PHASERphasing
REFMACrefinement
xia2data reduction
xia2data scaling