6YJV | pdb_00006yjv

Crystal structure of unliganded MGAT5 (alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase V) luminal domain with a Lys329-Ile345 loop truncation, in complex with UDP-2-deoxy-2-fluoroglucose and 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
Crystal Properties
Matthews coefficientSolvent content
2.2344.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.52α = 108.42
b = 69.21β = 92.25
c = 90.65γ = 106.54
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2019-05-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.97625DiamondI03

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
11.744.1494.70.0440.0280.99911.13.5106002
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)
11.71.741.0850.7050.5471

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)Mean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE5zic1.744.14106001366394.6570.1770.17540.180.21150.2243.149
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]
-2.1770.272-0.5451.3711.706-0.719
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.923
r_dihedral_angle_4_deg17.603
r_dihedral_angle_3_deg15.265
r_lrange_other8.394
r_lrange_it8.392
r_dihedral_angle_1_deg7.07
r_scangle_other6.572
r_scangle_it6.569
r_mcangle_it4.733
r_mcangle_other4.733
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.923
r_dihedral_angle_4_deg17.603
r_dihedral_angle_3_deg15.265
r_lrange_other8.394
r_lrange_it8.392
r_dihedral_angle_1_deg7.07
r_scangle_other6.572
r_scangle_it6.569
r_mcangle_it4.733
r_mcangle_other4.733
r_scbond_it4.312
r_scbond_other4.299
r_mcbond_it3.457
r_mcbond_other3.456
r_angle_refined_deg1.588
r_angle_other_deg1.274
r_symmetry_nbd_refined0.233
r_nbd_other0.225
r_symmetry_xyhbond_nbd_refined0.209
r_nbd_refined0.202
r_symmetry_nbd_other0.177
r_nbtor_refined0.163
r_xyhbond_nbd_refined0.163
r_ncsr_local_group_10.088
r_symmetry_nbtor_other0.08
r_chiral_restr0.078
r_symmetry_xyhbond_nbd_other0.072
r_bond_refined_d0.009
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 Atoms8127
Nucleic Acid Atoms
Solvent Atoms509
Heterogen Atoms184

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
REFMACphasing