6YJS

Crystal structure of MGAT5 (alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase V) luminal domain with a Lys329-Ile345 loop truncation, in complex with biantennary pentasaccharide M592


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5ZIC 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.1 M HEPES pH 8.0, 0.3 M Li2SO4, 30 % (w/v) PEG 3350, 10 % (v/v) ethylene glycol wXHPcQHrME
Crystal Properties
Matthews coefficientSolvent content
2.1643.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.28α = 108.81
b = 67.37β = 92.2
c = 91.05γ = 106.72
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293PIXELDECTRIS PILATUS 6M-F2019-02-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9795DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)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
11.642.5296.20.0540.0340.99910.43.5125194
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.641.1620.7220.5241.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE5zic1.642.52125193377096.1910.1850.18410.214534.716
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]
-0.3941.502-0.0522.302-0.13-2.354
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.234
r_dihedral_angle_4_deg18.091
r_dihedral_angle_3_deg14.646
r_lrange_it8.288
r_lrange_other8.258
r_dihedral_angle_1_deg6.756
r_scangle_it6.605
r_scangle_other6.603
r_scbond_it4.24
r_mcangle_it4.224
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.234
r_dihedral_angle_4_deg18.091
r_dihedral_angle_3_deg14.646
r_lrange_it8.288
r_lrange_other8.258
r_dihedral_angle_1_deg6.756
r_scangle_it6.605
r_scangle_other6.603
r_scbond_it4.24
r_mcangle_it4.224
r_mcangle_other4.224
r_scbond_other4.219
r_mcbond_it2.888
r_mcbond_other2.888
r_angle_refined_deg1.62
r_angle_other_deg1.291
r_nbd_other0.242
r_symmetry_nbd_refined0.234
r_nbd_refined0.2
r_symmetry_xyhbond_nbd_refined0.197
r_symmetry_nbd_other0.186
r_xyhbond_nbd_refined0.173
r_nbtor_refined0.167
r_symmetry_nbtor_other0.087
r_ncsr_local_group_10.087
r_xyhbond_nbd_other0.082
r_chiral_restr0.081
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7738
Nucleic Acid Atoms
Solvent Atoms466
Heterogen Atoms246

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
REFMACphasing