☰ Navigation Tabs
Wild type hexamer oxalyl-CoA synthetase (OCS)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8AFF
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 4.087 f_angle_d 0.4821 f_chiral_restr 0.0443 f_plane_restr 0.0043 f_bond_d 0.002
Sample Hexameric complex of the oxalyl-CoA synthetase Pcs60p
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument GATAN CRYOPLUNGE 3 Cryogen Name ETHANE Sample Vitrification Details 90% humidity in the sample chamber.
Gentle Blot function, 2.5 seconds
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 819000 Reported Resolution (Å) 3.1 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C2
Map-Model Fitting and Refinement Id 1 (8AFF) Refinement Space REAL Refinement Protocol RIGID BODY FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K2 QUANTUM (4k x 4k) Electron Dose (electrons/Å**2) 63
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 700 Maximum Defocus (nm) 2200 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 0.01 Imaging Mode BRIGHT FIELD Specimen Holder Model FEI TITAN KRIOS AUTOGRID HOLDER Nominal Magnification 105000 Calibrated Magnification 105000 Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION crYOLO beta IMAGE ACQUISITION EPU 1.2 CTF CORRECTION Gctf 1.02 MODEL FITTING UCSF Chimera 1.15 MODEL REFINEMENT PHENIX 1.1 MODEL REFINEMENT Coot 0.9.4 INITIAL EULER ASSIGNMENT SPHIRE 1.2 FINAL EULER ASSIGNMENT SPHIRE 1.3 RECONSTRUCTION SPHIRE 1.3
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 4000000 Picking was performed using cryOLO