3Q7I

Glucose-6-phosphate isomerase from Francisella tularensis complexed with 6-phosphogluconic acid.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3LJKPDB entry 3LJK

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP62890.2 M Ca(OAc)2, 0.1 M MES buffer, 10% 2-propanol, 0.01 M 6-phosphogluconic acid., pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.5952.57

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 114.439α = 90
b = 114.439β = 90
c = 84.319γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152010-03-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.9792APS19-ID

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
11.5437.599.90.06711.310935419354128.2
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)
1.541.571000.7942.155.64616

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 3LJK1.5437.469335093350468499.540.14580.14580.14450.1707RANDOM24.138
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]
-0.72-0.36-0.721.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.194
r_dihedral_angle_4_deg17.804
r_dihedral_angle_3_deg13.926
r_dihedral_angle_1_deg5.885
r_scangle_it4.422
r_scbond_it2.72
r_angle_refined_deg1.853
r_mcangle_it1.698
r_angle_other_deg1.018
r_mcbond_it0.993
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.194
r_dihedral_angle_4_deg17.804
r_dihedral_angle_3_deg13.926
r_dihedral_angle_1_deg5.885
r_scangle_it4.422
r_scbond_it2.72
r_angle_refined_deg1.853
r_mcangle_it1.698
r_angle_other_deg1.018
r_mcbond_it0.993
r_mcbond_other0.321
r_chiral_restr0.115
r_bond_refined_d0.019
r_gen_planes_refined0.01
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4312
Nucleic Acid Atoms
Solvent Atoms528
Heterogen Atoms51

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
HKL-3000phasing