4JBB

Crystal structure of Glutathione S-transferase A6TBY7(Target EFI-507184) from Klebsiella pneumoniae MGH 78578, GSH complex


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3BBYPDB ENTRY 3BBY

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
173.5M SODIUM PHORMATE, PH 7.0 VAPOR DIFFUSION, SITTING DROP
Crystal Properties
Matthews coefficientSolvent content
2.4650.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.897α = 90
b = 67.897β = 90
c = 97.547γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315MIRRORS2012-02-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29A1.075NSLSX29A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.485098.90.05912.96.343402-3
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)
11.481.511000.6012.46.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3BBY1.4837.5742048135598.880.109010.108340.13078RANDOM29.703
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]
0.340.340.34-1.1
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free37.824
r_dihedral_angle_2_deg34.624
r_dihedral_angle_4_deg18.277
r_sphericity_bonded16.901
r_dihedral_angle_3_deg11.097
r_dihedral_angle_1_deg5.243
r_rigid_bond_restr4.091
r_angle_refined_deg1.245
r_angle_other_deg1.159
r_chiral_restr0.104
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free37.824
r_dihedral_angle_2_deg34.624
r_dihedral_angle_4_deg18.277
r_sphericity_bonded16.901
r_dihedral_angle_3_deg11.097
r_dihedral_angle_1_deg5.243
r_rigid_bond_restr4.091
r_angle_refined_deg1.245
r_angle_other_deg1.159
r_chiral_restr0.104
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.002
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_it
r_mcbond_other
r_mcangle_it
r_scbond_it
r_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1651
Nucleic Acid Atoms
Solvent Atoms297
Heterogen Atoms24

Software

Software
Software NamePurpose
PHASERphasing
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling