4N0V

Crystal structure of a glutathione S-transferase domain-containing protein (Marinobacter aquaeolei VT8), Target EFI-507332


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52730.2M Sodium Chloride, 0.1 M Tris:HCl, 25% PEG3350, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 273K
Crystal Properties
Matthews coefficientSolvent content
2.3547.76

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.607α = 90
b = 70.784β = 90
c = 98.776γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225HE2013-06-14MSINGLE 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 Merge 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
11.75099.60.06727.97.25227152068
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)
11.71.7399.80.712.97.2

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 3ERF1.75049347265899.480.19490.193480.22059RANDOM28.704
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]
1.59-0.98-0.6
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.93
r_dihedral_angle_4_deg14.94
r_dihedral_angle_3_deg11.889
r_long_range_B_refined6.926
r_long_range_B_other6.836
r_dihedral_angle_1_deg5.652
r_scangle_other5.639
r_mcangle_it3.979
r_mcangle_other3.979
r_scbond_it3.952
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.93
r_dihedral_angle_4_deg14.94
r_dihedral_angle_3_deg11.889
r_long_range_B_refined6.926
r_long_range_B_other6.836
r_dihedral_angle_1_deg5.652
r_scangle_other5.639
r_mcangle_it3.979
r_mcangle_other3.979
r_scbond_it3.952
r_scbond_other3.951
r_mcbond_it2.897
r_mcbond_other2.894
r_angle_refined_deg1.406
r_angle_other_deg0.894
r_chiral_restr0.097
r_bond_refined_d0.013
r_gen_planes_refined0.013
r_gen_planes_other0.006
r_bond_other_d0.004
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 Atoms3190
Nucleic Acid Atoms
Solvent Atoms218
Heterogen Atoms

Software

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