6ZJ9

Crystal structure of Equus ferus caballus glutathione transferase A3-3 in complex with glutathione


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1TDI 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52940.1 M Bicine/Trizma base pH 8.5, 10% w/v PEG 20 000, 20% v/v PEG MME 550, and 0.02 M of each alcohol (1,6-hexanediol, 1-butanol, (RS)-1,2-propanediol, 2-propanol, 1,4-butanediol, and 1,3-propanediol)
Crystal Properties
Matthews coefficientSolvent content
2.5952.43

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.907α = 90
b = 99.154β = 90
c = 48.186γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2019-04-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.91587DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
12.299.1599.90.1660.1760.0580.9937.58.313931
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.2799.20.5450.5960.2370.9015.9

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 REPLACEMENTTHROUGHOUT1tdi2.249.581322567199.910.16780.16470.2285RANDOM31.679
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]
-0.94-3.54.43
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.246
r_dihedral_angle_4_deg16.488
r_dihedral_angle_3_deg14.483
r_dihedral_angle_1_deg6.134
r_angle_other_deg2.23
r_angle_refined_deg1.737
r_chiral_restr0.094
r_bond_other_d0.033
r_gen_planes_other0.016
r_bond_refined_d0.012
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.246
r_dihedral_angle_4_deg16.488
r_dihedral_angle_3_deg14.483
r_dihedral_angle_1_deg6.134
r_angle_other_deg2.23
r_angle_refined_deg1.737
r_chiral_restr0.094
r_bond_other_d0.033
r_gen_planes_other0.016
r_bond_refined_d0.012
r_gen_planes_refined0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1769
Nucleic Acid Atoms
Solvent Atoms103
Heterogen Atoms36

Software

Software
Software NamePurpose
Aimlessdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
DIALSdata reduction