4MF7 | pdb_00004mf7

Crystal structure of glutathione transferase BBTA-3750 from Bradyrhizobium sp., Target EFI-507290


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4IKHPDB ENTRY 4IKH

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.9298protein in 10 MM HEPES, pH 7.5, 150 mM sodium chloride, 5% glycerol, reservoir: 0.2 M potassium nitrate, pH 6.9, 20% PEG3350, cryoprotectant: 20% diethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.3547.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.526α = 90
b = 88.951β = 90
c = 78.127γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225HEmirrors2013-08-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 31-IDAPS31-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.85099.90.0710.07113.87.425702-5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.831000.80.82.87.4

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 4IKH1.8502485082999.850.178210.176930.190.218580.23RANDOM40.306
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]
-1.11.29-0.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.819
r_dihedral_angle_3_deg13.692
r_long_range_B_other12.671
r_long_range_B_refined12.525
r_scangle_other12.409
r_scbond_other11.816
r_scbond_it11.796
r_dihedral_angle_4_deg8.033
r_mcangle_it7.621
r_mcangle_other7.618
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.819
r_dihedral_angle_3_deg13.692
r_long_range_B_other12.671
r_long_range_B_refined12.525
r_scangle_other12.409
r_scbond_other11.816
r_scbond_it11.796
r_dihedral_angle_4_deg8.033
r_mcangle_it7.621
r_mcangle_other7.618
r_mcbond_it7.6
r_mcbond_other7.596
r_dihedral_angle_1_deg5.83
r_angle_refined_deg1.361
r_angle_other_deg0.838
r_chiral_restr0.081
r_bond_refined_d0.011
r_gen_planes_refined0.007
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1627
Nucleic Acid Atoms
Solvent Atoms173
Heterogen Atoms

Software

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