4IQ1

Crystal structure of glutathione s-transferase MHA_0454 (TARGET EFI-507015) FROM Mannheimia haemolytica, SUBSTRATE-FREE


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2X64 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.52940.1M BIS-TRIS, PH 5.5, 0.2M LITHIUM SULFATE, 25% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
2.4850.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.019α = 90
b = 81.776β = 90
c = 288.652γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225HEMIRRORS2012-12-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 31-ID0.9793APS31-ID

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
11.855091.30.0937.96.16140061400-327.01
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)
11.851.8893.20.862.46.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2X641.8537.665943659436188291.240.17620.176270.173980.24701RANDOM38.033
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]
0.5-0.4-0.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.279
r_sphericity_free23.124
r_sphericity_bonded21.327
r_dihedral_angle_4_deg20.424
r_dihedral_angle_3_deg15.494
r_dihedral_angle_1_deg5.7
r_rigid_bond_restr4.272
r_angle_refined_deg1.333
r_chiral_restr0.098
r_bond_refined_d0.011
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.279
r_sphericity_free23.124
r_sphericity_bonded21.327
r_dihedral_angle_4_deg20.424
r_dihedral_angle_3_deg15.494
r_dihedral_angle_1_deg5.7
r_rigid_bond_restr4.272
r_angle_refined_deg1.333
r_chiral_restr0.098
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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 Atoms5050
Nucleic Acid Atoms
Solvent Atoms382
Heterogen Atoms8

Software

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