1USB

Rational design of a novel enzyme - efficient thioester hydrolysis enabled by the incorporation of a single His residue into human glutathione transferase A1-1


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1GSDPDB ENTRY 1GSD

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.80.1 M TRISHCL PH 7.8, 26 % PEG4000, 2 MM DITHIOTHREITOL
Crystal Properties
Matthews coefficientSolvent content
2.340.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 98.906α = 90
b = 92.05β = 93.21
c = 51.272γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHBENT MIRROR2003-03-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX II BEAMLINE I711MAX III711

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
12.0767.42990.0936.65415.022801124.7
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)
12.072.1893.40.292.433.17

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB ENTRY 1GSD2.074028008141199.60.1920.1890.245RANDOM27.79
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]
0.491.530.58-0.9
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.488
r_scangle_it4.007
r_scbond_it2.479
r_mcangle_it1.728
r_angle_refined_deg1.603
r_angle_other_deg1.026
r_mcbond_it0.967
r_nbd_refined0.244
r_nbd_other0.243
r_metal_ion_refined0.229
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.488
r_scangle_it4.007
r_scbond_it2.479
r_mcangle_it1.728
r_angle_refined_deg1.603
r_angle_other_deg1.026
r_mcbond_it0.967
r_nbd_refined0.244
r_nbd_other0.243
r_metal_ion_refined0.229
r_symmetry_hbond_refined0.201
r_symmetry_vdw_refined0.197
r_symmetry_vdw_other0.196
r_xyhbond_nbd_refined0.166
r_chiral_restr0.165
r_nbtor_other0.088
r_bond_refined_d0.018
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3547
Nucleic Acid Atoms
Solvent Atoms259
Heterogen Atoms44

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling