6YJT | pdb_00006yjt

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


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
2.2545.43

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.03α = 107.77
b = 69.59β = 91.81
c = 90γ = 106.94
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2019-04-08MSINGLE 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
11.743.43960.0470.030.9999.93.6108811
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)
11.71.741.3460.8040.5621

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-VALUE5zic1.743.43104711372795.6430.1860.18450.190.22280.2354.886
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]
-3.171.4761.5111.7443.277-2.346
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.194
r_dihedral_angle_4_deg16.022
r_dihedral_angle_3_deg14.595
r_lrange_other9.344
r_lrange_it9.335
r_scangle_it7.598
r_scangle_other7.594
r_dihedral_angle_1_deg7.055
r_mcangle_other5.608
r_mcangle_it5.607
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.194
r_dihedral_angle_4_deg16.022
r_dihedral_angle_3_deg14.595
r_lrange_other9.344
r_lrange_it9.335
r_scangle_it7.598
r_scangle_other7.594
r_dihedral_angle_1_deg7.055
r_mcangle_other5.608
r_mcangle_it5.607
r_scbond_it5.149
r_scbond_other5.121
r_mcbond_it4.187
r_mcbond_other4.182
r_angle_refined_deg1.536
r_angle_other_deg1.255
r_nbd_other0.228
r_symmetry_xyhbond_nbd_refined0.206
r_symmetry_nbd_refined0.194
r_nbd_refined0.192
r_symmetry_nbd_other0.18
r_nbtor_refined0.164
r_xyhbond_nbd_refined0.154
r_ncsr_local_group_10.088
r_symmetry_nbtor_other0.078
r_chiral_restr0.074
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8218
Nucleic Acid Atoms
Solvent Atoms330
Heterogen Atoms140

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing