3V0O

Crystal structure of the Fucosylgalactoside alpha N-acetylgalactosaminyltransferase (GTA, cisAB mutant L266G, G268A) in complex with a novel UDP-GalNAc derived inhibitor (4GW) and H-antigen acceptor


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 295.0
Details 50 mM MOPS pH 7, 50-200 mM AMMONIUM SULFATE, 50 mM MnCl2, AND 6-9% PEG-3350 , VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 74.23 α = 90
b = 151.68 β = 90
c = 52.18 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RAYONIX MX-225 mirrors 2010-01-15
Diffraction Radiation
Monochromator Protocol
Double Crystal Monochromator, Si-111 crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON BESSY BEAMLINE 14.1 0.91841 BESSY 14.1

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
1.65 20 97.8 0.076 -- -- 7.1 71749 70167 -- -3.0 26.606
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)
1.65 1.8 96.8 0.707 -- 2.91 7.0 16243

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 1.65 19.664 -- 1.99 -- 70164 2105 97.85 -- 0.1584 0.1572 0.194 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 1.65 1.6883 4555 136 4421 0.2241 0.2429 -- 97.0
X Ray Diffraction 1.6883 1.7305 4534 136 4398 0.2103 0.2579 -- 97.0
X Ray Diffraction 1.7305 1.7773 4585 138 4447 0.1967 0.2403 -- 97.0
X Ray Diffraction 1.7773 1.8295 4612 138 4474 0.1856 0.2154 -- 97.0
X Ray Diffraction 1.8295 1.8886 4617 139 4478 0.1645 0.2093 -- 98.0
X Ray Diffraction 1.8886 1.956 4604 138 4466 0.1612 0.1887 -- 97.0
X Ray Diffraction 1.956 2.0342 4631 139 4492 0.1544 0.214 -- 98.0
X Ray Diffraction 2.0342 2.1267 4643 139 4504 0.1529 0.2094 -- 98.0
X Ray Diffraction 2.1267 2.2387 4671 140 4531 0.1534 0.1841 -- 98.0
X Ray Diffraction 2.2387 2.3787 4669 140 4529 0.1466 0.204 -- 98.0
X Ray Diffraction 2.3787 2.562 4727 142 4585 0.1547 0.1932 -- 99.0
X Ray Diffraction 2.562 2.8192 4687 141 4546 0.1611 0.2067 -- 98.0
X Ray Diffraction 2.8192 3.2256 4788 143 4645 0.1645 0.2015 -- 99.0
X Ray Diffraction 3.2256 4.058 4802 144 4658 0.1435 0.1871 -- 99.0
X Ray Diffraction 4.058 19.6651 5037 152 4885 0.1441 0.158 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic+tls
Mean Isotropic B 22.856
Anisotropic B[1][1] -0.4352
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.1555
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.5906
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 15.595
f_plane_restr 0.008
f_chiral_restr 0.098
f_angle_d 1.437
f_bond_d 0.012
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4706
Nucleic Acid Atoms 0
Heterogen Atoms 131
Solvent Atoms 469

Software

Computing
Computing Package Purpose
mxCuBE Data Collection
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.7.1_743) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
phenix refinement
Phaser version: 2.1.4 molecular replacement
Xscale data reduction