6YJQ | pdb_00006yjq

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


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
1.5520.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47α = 108.36
b = 68.17β = 92.28
c = 90.99γ = 106.86
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2019-01-22MSINGLE 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
11.943.31970.0660.0420.9979.93.577533
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)
11.91.951.1590.7210.4221.2

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)Mean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE5zic1.943.3177533368496.940.1960.19410.20.23710.2446.468
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]
-0.2110.5570.3041.1851.592-2.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.22
r_dihedral_angle_4_deg17.018
r_dihedral_angle_3_deg14.703
r_lrange_it7.646
r_lrange_other7.624
r_dihedral_angle_1_deg6.834
r_scangle_it6.132
r_scangle_other6.113
r_mcangle_it4.795
r_mcangle_other4.794
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.22
r_dihedral_angle_4_deg17.018
r_dihedral_angle_3_deg14.703
r_lrange_it7.646
r_lrange_other7.624
r_dihedral_angle_1_deg6.834
r_scangle_it6.132
r_scangle_other6.113
r_mcangle_it4.795
r_mcangle_other4.794
r_scbond_it4.163
r_scbond_other4.132
r_mcbond_it3.599
r_mcbond_other3.598
r_angle_refined_deg1.457
r_angle_other_deg1.252
r_symmetry_nbd_refined0.206
r_nbd_refined0.199
r_nbd_other0.195
r_symmetry_nbd_other0.172
r_nbtor_refined0.164
r_xyhbond_nbd_refined0.154
r_symmetry_xyhbond_nbd_refined0.115
r_ncsr_local_group_10.088
r_symmetry_xyhbond_nbd_other0.084
r_symmetry_nbtor_other0.076
r_chiral_restr0.071
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 Atoms7989
Nucleic Acid Atoms
Solvent Atoms287
Heterogen Atoms96

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
MOLREPphasing