3ZGF

Crystal structure of the Fucosylgalactoside alpha N- acetylgalactosaminyltransferase (GTA, cisAB mutant L266G, G268A) in complex with in complex with NPE caged UDP-Gal (P2(1)2(1)2(1) space group)


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 7
Details 7-12% POLYETHYLENE GLYCOL 3350, 0.1 - 0.3 M AMMONIUM SULPHATE, 0.05 M MNCL2, 0.05 M MOPS PH 7.0

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 52.84 α = 90
b = 78.45 β = 90
c = 155.13 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH SX-165 MULTILAYER MIRROR --
Diffraction Radiation
Monochromator Protocol
BENT SI (220) CRYSTAL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON MAX II BEAMLINE I911-5 -- MAX_II I911-5

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
1.7 20 99.0 0.08 -- -- 7.0 -- 71207 -- 2.96 20.24
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)
1.7 1.85 96.2 0.63 -- 2.96 6.3 --

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 1.701 19.984 -- 1.99 -- 71129 2134 99.34 -- 0.1827 0.1816 0.2173 --
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 1.7012 1.7407 -- 127 4110 0.3378 0.4186 -- 90.0
X Ray Diffraction 1.7407 1.7842 -- 143 4589 0.2727 0.2917 -- 100.0
X Ray Diffraction 1.7842 1.8325 -- 141 4555 0.2394 0.3003 -- 100.0
X Ray Diffraction 1.8325 1.8863 -- 141 4583 0.2175 0.2486 -- 100.0
X Ray Diffraction 1.8863 1.9472 -- 140 4559 0.2086 0.2634 -- 100.0
X Ray Diffraction 1.9472 2.0167 -- 143 4612 0.1922 0.2187 -- 100.0
X Ray Diffraction 2.0167 2.0974 -- 141 4571 0.1877 0.2692 -- 100.0
X Ray Diffraction 2.0974 2.1927 -- 143 4609 0.1887 0.2428 -- 100.0
X Ray Diffraction 2.1927 2.3082 -- 143 4625 0.1798 0.2432 -- 100.0
X Ray Diffraction 2.3082 2.4525 -- 142 4591 0.1848 0.2142 -- 100.0
X Ray Diffraction 2.4525 2.6415 -- 142 4658 0.183 0.2368 -- 100.0
X Ray Diffraction 2.6415 2.9066 -- 144 4640 0.1892 0.2332 -- 100.0
X Ray Diffraction 2.9066 3.3255 -- 144 4659 0.1775 0.2223 -- 100.0
X Ray Diffraction 3.3255 4.1835 -- 147 4721 0.1564 0.1744 -- 100.0
X Ray Diffraction 4.1835 19.9853 -- 153 4913 0.1493 0.1582 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -0.1346
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.0282
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.1064
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 15.496
f_chiral_restr 0.079
f_bond_d 0.009
f_angle_d 1.107
f_plane_restr 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4697
Nucleic Acid Atoms 0
Heterogen Atoms 83
Solvent Atoms 527

Software

Software
Software Name Purpose
PHENIX refinement version: (PHENIX.REFINE)
XDS data reduction
SCALA data scaling
PHASER phasing