☰ Navigation Tabs
GT-C O-Mannosyltransferase TMEM260 co-purified with natural donor and in complex with acceptor peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold Q9NX78
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 10.3238 f_angle_d 0.9045 f_chiral_restr 0.0885 f_plane_restr 0.0121 f_bond_d 0.0067
Sample protein-specific O-mannosyl-transferase (TMEM260) incubated with Synthetic peptide derived from PLXNB2 IPT1 domain
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 271859 Reported Resolution (Å) 3.06 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 Refinement Space REAL Refinement Protocol FLEXIBLE FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 BIOQUANTUM (6k x 4k) Electron Dose (electrons/Å**2) 49.8
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 500 Maximum Defocus (nm) 2000 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2.7 Imaging Mode BRIGHT FIELD Specimen Holder Model OTHER Nominal Magnification 105000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC v4.7.0 IMAGE ACQUISITION EPU CTF CORRECTION cryoSPARC v4.7.0 MODEL FITTING UCSF Chimera MODEL FITTING PHENIX MODEL FITTING Coot INITIAL EULER ASSIGNMENT cryoSPARC v4.7.0 FINAL EULER ASSIGNMENT cryoSPARC v4.7.0 CLASSIFICATION cryoSPARC v4.7.0 RECONSTRUCTION cryoSPARC v4.7.0 MODEL REFINEMENT PHENIX
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION