8CE3 | pdb_00008ce3

Crystal structure of MGAT5 (alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase V) luminal domain with a Lys329-Ile345 loop truncation, in complex with 3D fragment 2548


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6YJTsame protein with a different ligand

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
2.2545.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.86α = 107.3
b = 68.54β = 92.16
c = 91.31γ = 107.05
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2019-03-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.95DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim 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
11.8960.4797.260.047113.63.580017
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.891.921.2970.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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-VALUE1.8960.46580017379597.2590.1920.18970.20.23270.2454.819
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]
-0.2581.0250.567-0.0621.78-1.538
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg15.501
r_dihedral_angle_3_deg15.187
r_lrange_it10.513
r_lrange_other10.512
r_scangle_it9.087
r_scangle_other9.087
r_dihedral_angle_1_deg6.898
r_mcangle_it6.839
r_mcangle_other6.839
r_scbond_it6.459
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg15.501
r_dihedral_angle_3_deg15.187
r_lrange_it10.513
r_lrange_other10.512
r_scangle_it9.087
r_scangle_other9.087
r_dihedral_angle_1_deg6.898
r_mcangle_it6.839
r_mcangle_other6.839
r_scbond_it6.459
r_scbond_other6.459
r_dihedral_angle_2_deg6.242
r_mcbond_it5.456
r_mcbond_other5.456
r_angle_refined_deg1.51
r_angle_other_deg0.487
r_xyhbond_nbd_refined0.265
r_nbd_refined0.218
r_symmetry_xyhbond_nbd_refined0.201
r_symmetry_nbd_other0.197
r_nbd_other0.19
r_nbtor_refined0.184
r_symmetry_nbd_refined0.176
r_symmetry_xyhbond_nbd_other0.137
r_ncsr_local_group_10.102
r_symmetry_nbtor_other0.081
r_chiral_restr0.074
r_gen_planes_refined0.009
r_bond_refined_d0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8033
Nucleic Acid Atoms
Solvent Atoms349
Heterogen Atoms112

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
REFMACphasing