6YJR

Crystal structure of unliganded MGAT5 (alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase V) luminal domain.


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 Citrate pH 5.0 16% w/v PEG6000
Crystal Properties
Matthews coefficientSolvent content
2.5852.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.809α = 90
b = 100.415β = 90
c = 207.981γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2018-03-10MSINGLE 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
12.19848.8193.40.1220.0470.99812.37.836979
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)
12.22.491.2230.4790.6151.7

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-VALUE5zic2.19848.8135113186657.0850.2110.20810.262570.676
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]
-2.51710.152-7.636
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.424
r_dihedral_angle_4_deg18.034
r_dihedral_angle_3_deg17.643
r_lrange_it7.371
r_lrange_other7.369
r_dihedral_angle_1_deg7.238
r_scangle_it5.548
r_scangle_other5.547
r_mcangle_it4.779
r_mcangle_other4.779
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.424
r_dihedral_angle_4_deg18.034
r_dihedral_angle_3_deg17.643
r_lrange_it7.371
r_lrange_other7.369
r_dihedral_angle_1_deg7.238
r_scangle_it5.548
r_scangle_other5.547
r_mcangle_it4.779
r_mcangle_other4.779
r_scbond_it3.52
r_scbond_other3.52
r_mcbond_it3.181
r_mcbond_other3.18
r_angle_refined_deg1.572
r_angle_other_deg1.246
r_symmetry_xyhbond_nbd_refined0.311
r_nbd_other0.232
r_nbd_refined0.214
r_symmetry_xyhbond_nbd_other0.208
r_symmetry_nbd_refined0.198
r_symmetry_nbd_other0.185
r_nbtor_refined0.172
r_xyhbond_nbd_refined0.147
r_ncsr_local_group_10.089
r_symmetry_nbtor_other0.08
r_chiral_restr0.068
r_bond_refined_d0.009
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7886
Nucleic Acid Atoms
Solvent Atoms88
Heterogen Atoms78

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
STARANISOdata scaling
MOLREPphasing