4JED

Crystal structure of glutathione s-transferase mrad2831_1084 (target efi-507060) from methylobacterium radiotolerans jcm 2831, complex with glutathione sulfonate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4JBBPDB ENTRY 4JBB

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.51M LITHIUM CHLORIDE, 0.1M SODIUM ACETATE, 30% PEG6000, 5mM GSH , pH 7.5, VAPOR DIFFUSION, SITTING DROP
Crystal Properties
Matthews coefficientSolvent content
1.9637.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.664α = 90
b = 54.217β = 90
c = 55.147γ = 90
Symmetry
Space GroupP 21 21 2

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 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
11.15090.60.06412.4877540-5
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)
11.11.1239.80.71424.4

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 4JBB1.133.8375900154490.690.114810.114470.13072RANDOM14.616
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]
-0.68-0.571.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg22.483
r_sphericity_free21.96
r_dihedral_angle_4_deg17.298
r_dihedral_angle_3_deg9.591
r_rigid_bond_restr8.804
r_sphericity_bonded7.669
r_dihedral_angle_1_deg5.489
r_angle_refined_deg1.568
r_angle_other_deg0.817
r_chiral_restr0.284
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg22.483
r_sphericity_free21.96
r_dihedral_angle_4_deg17.298
r_dihedral_angle_3_deg9.591
r_rigid_bond_restr8.804
r_sphericity_bonded7.669
r_dihedral_angle_1_deg5.489
r_angle_refined_deg1.568
r_angle_other_deg0.817
r_chiral_restr0.284
r_bond_refined_d0.011
r_gen_planes_refined0.009
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_mcbond_it
r_mcbond_other
r_mcangle_it
r_scbond_it
r_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1682
Nucleic Acid Atoms
Solvent Atoms398
Heterogen Atoms29

Software

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