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GT-C O-Mannosyltransferase TMEM260 incubated with Far-P-Man
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 11.1101 f_angle_d 0.8307 f_chiral_restr 0.0756 f_plane_restr 0.0102 f_bond_d 0.0084
Sample protein-specific O-mannosyl-transferase (TMEM260) incubated with Far-P-Man
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 332040 Reported Resolution (Å) 2.65 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) 60.1
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 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