4NAX

Crystal structure of glutathione transferase PPUT_1760 from Pseudomonas putida, target EFI-507288, with one glutathione disulfide bound per one protein subunit


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4MF6PDB ENTRY 4MF6

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17Protein in 10 mM HEPES, PH 7.5, 150 mM sodium chloride, 5% glycerol, reservoir: 20% peg1500, 20% glycerol, 5 MM GSH, cryoprotectant: NONE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K
Crystal Properties
Matthews coefficientSolvent content
2.0740.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.342α = 90
b = 66.62β = 90
c = 119.821γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315MIRRORS2013-10-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29ANSLSX29A

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
11.35099.90.0949.77.9116741-5
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)
11.31.321000.662.57.7

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 4MF61.30150113148350299.710.101460.100530.13123RANDOM21.927
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]
0.64-0.45-0.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.304
r_sphericity_free26.756
r_sphericity_bonded16.532
r_dihedral_angle_3_deg11.814
r_dihedral_angle_4_deg10.924
r_rigid_bond_restr10.918
r_scbond_other7.506
r_scbond_it7.505
r_scangle_other7.453
r_long_range_B_refined5.955
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.304
r_sphericity_free26.756
r_sphericity_bonded16.532
r_dihedral_angle_3_deg11.814
r_dihedral_angle_4_deg10.924
r_rigid_bond_restr10.918
r_scbond_other7.506
r_scbond_it7.505
r_scangle_other7.453
r_long_range_B_refined5.955
r_long_range_B_other5.954
r_dihedral_angle_1_deg5.632
r_mcbond_it3.218
r_mcbond_other3.217
r_mcangle_it3.135
r_mcangle_other3.135
r_angle_refined_deg1.431
r_angle_other_deg0.854
r_chiral_restr0.094
r_bond_refined_d0.009
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
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_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3771
Nucleic Acid Atoms
Solvent Atoms543
Heterogen Atoms101

Software

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