3Q88

Glucose-6-phosphate isomerase from Francisella tularensis complexed with ribose 1,5-bisphosphate.


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 5-phospho-alpha-D-ribose 1-diphosphate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.652.69

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 114.465α = 90
b = 114.465β = 90
c = 84.5γ = 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
11.7341000.10810.18.2705717057133
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)
1.71.731000.8222.697.73489

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 3LJK1.733.997037370373352199.660.14760.14760.14620.1739RANDOM27.076
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]
-0.47-0.24-0.470.71
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.266
r_dihedral_angle_4_deg16.309
r_dihedral_angle_3_deg15.047
r_dihedral_angle_1_deg5.797
r_scangle_it4.345
r_scbond_it2.652
r_mcangle_it1.697
r_angle_refined_deg1.695
r_angle_other_deg0.994
r_mcbond_it0.982
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.266
r_dihedral_angle_4_deg16.309
r_dihedral_angle_3_deg15.047
r_dihedral_angle_1_deg5.797
r_scangle_it4.345
r_scbond_it2.652
r_mcangle_it1.697
r_angle_refined_deg1.695
r_angle_other_deg0.994
r_mcbond_it0.982
r_mcbond_other0.32
r_chiral_restr0.111
r_bond_refined_d0.019
r_gen_planes_refined0.009
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 Atoms483
Heterogen Atoms52

Software

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