4KH7

Crystal structure of a glutathione transferase family member from salmonella enterica ty2, target efi-507262, with bound glutathione


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7
Temperature 298.0
Details Protein (10 mM Hepes pH 7.5, 150 mM NaCl, 5% glycerol, 5 mM GSH), Reservoir (0.1 M Bis-Tris Propane pH 7, 1.2 M Potassium Sodium Tartrate Tetrahydrate), Cryoprotection (reservoir + 20% glycerol), vapor diffusion, sitting drop, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 53.08 α = 90
b = 72.69 β = 96.15
c = 82.9 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RAYONIX MX225HE MIRRORS 2013-04-17
Diffraction Radiation
Monochromator Protocol
GRAPHITE SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 31-ID 0.9793 APS 31-ID

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
1.5 82.42 99.5 0.054 0.054 -- 3.7 99706 99706 0.0 0.0 15.85
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
1.5 1.58 100.0 0.65 0.65 1.2 3.7 14564

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MOLECULAR REPLACEMENT 1.5 36.346 0.0 0.0 99661 99661 4974 99.48 0.1714 0.1714 0.1706 0.1873 RANDOM
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 1.5 1.517 -- 174 3175 0.2931 0.3333 -- 100.0
X Ray Diffraction 1.517 1.5349 -- 165 3153 0.2783 0.2929 -- 100.0
X Ray Diffraction 1.5349 1.5536 -- 169 3107 0.2729 0.2605 -- 100.0
X Ray Diffraction 1.5536 1.5733 -- 153 3184 0.2505 0.274 -- 100.0
X Ray Diffraction 1.5733 1.594 -- 151 3168 0.2539 0.2683 -- 100.0
X Ray Diffraction 1.594 1.6158 -- 142 3189 0.242 0.2754 -- 100.0
X Ray Diffraction 1.6158 1.6389 -- 153 3163 0.2328 0.2958 -- 100.0
X Ray Diffraction 1.6389 1.6634 -- 182 3175 0.2158 0.2374 -- 100.0
X Ray Diffraction 1.6634 1.6894 -- 155 3130 0.2075 0.2592 -- 100.0
X Ray Diffraction 1.6894 1.7171 -- 177 3146 0.2042 0.2361 -- 100.0
X Ray Diffraction 1.7171 1.7467 -- 170 3159 0.2047 0.22 -- 100.0
X Ray Diffraction 1.7467 1.7784 -- 139 3228 0.2044 0.2267 -- 100.0
X Ray Diffraction 1.7784 1.8126 -- 172 3131 0.1942 0.2236 -- 100.0
X Ray Diffraction 1.8126 1.8496 -- 153 3141 0.189 0.2492 -- 100.0
X Ray Diffraction 1.8496 1.8898 -- 168 3171 0.1875 0.1826 -- 100.0
X Ray Diffraction 1.8898 1.9338 -- 168 3168 0.1855 0.1932 -- 100.0
X Ray Diffraction 1.9338 1.9822 -- 157 3156 0.1822 0.2011 -- 100.0
X Ray Diffraction 1.9822 2.0357 -- 188 3181 0.1659 0.1933 -- 100.0
X Ray Diffraction 2.0357 2.0956 -- 177 3146 0.1579 0.1746 -- 100.0
X Ray Diffraction 2.0956 2.1633 -- 160 3155 0.161 0.1695 -- 100.0
X Ray Diffraction 2.1633 2.2406 -- 187 3166 0.1607 0.182 -- 100.0
X Ray Diffraction 2.2406 2.3303 -- 164 3142 0.152 0.18 -- 99.0
X Ray Diffraction 2.3303 2.4363 -- 172 3165 0.1607 0.1986 -- 100.0
X Ray Diffraction 2.4363 2.5647 -- 185 3148 0.1527 0.1776 -- 99.0
X Ray Diffraction 2.5647 2.7254 -- 159 3158 0.1514 0.1732 -- 100.0
X Ray Diffraction 2.7254 2.9357 -- 159 3185 0.1497 0.1824 -- 99.0
X Ray Diffraction 2.9357 3.231 -- 172 3150 0.158 0.1965 -- 99.0
X Ray Diffraction 3.231 3.6981 -- 146 3160 0.1463 0.1479 -- 98.0
X Ray Diffraction 3.6981 4.6577 -- 166 3120 0.1324 0.1352 -- 97.0
X Ray Diffraction 4.6577 36.3567 -- 191 3067 0.1862 0.1711 -- 94.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 23.8735
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.008
f_chiral_restr 0.069
f_dihedral_angle_d 12.868
f_bond_d 0.01
f_angle_d 1.248
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3360
Nucleic Acid Atoms 0
Heterogen Atoms 40
Solvent Atoms 604

Software

Software
Software Name Purpose
SCALA data scaling version: 3.3.20
PHENIX refinement version: 1.8.1_1168
PDB_EXTRACT data extraction version: 3.11
MOSFLM data reduction
AMoRE phasing