ELECTRON MICROSCOPY

Sample

Human ATP citrate lyase (homotetramer)

Specimen Preperation
Sample Aggregation State PARTICLE
Vitrification Instrument LEICA EM GP
Cryogen Name ETHANE
Sample Vitrification Details Leica EM GP2
3D Reconstruction
Reconstruction Method SINGLE PARTICLE
Number of Particles 280072
Reported Resolution (Å) 3.25
Resolution Method FSC 0.143 CUT-OFF
Other Details Following 3D classification, local refinement resulted in a cryo-EM volume with a golden standard FSC0.143-resolution of 3.25 Angstrom in which the atomic models for the CSS and CSH modules (extracted from pdb 6xhx) were fitted using Chimera and real-space refined in Phenix using reference restraints to the starting model.
Refinement Type
Symmetry Type POINT
Map-Model Fitting and Refinement
ID 1
Refinement Space REAL
Refinement Protocol FLEXIBLE FIT
Refinement Target ?
Overall B Value 138.8
Fitting Procedure ?
Details Following 3D classification, local refinement resulted in a cryo-EM volume with a golden standard FSC0.143-resolution of 3.25 Angstrom in which the atomic models for the CSS and CSH modules (extracted from pdb 6xhx) were fitted using Chimera and real-space refined in Phenix using reference restraints to the starting model. Cryo-EM map regions representing ligands in the ATP-grasp fold domain of the CCS module and in the CoA-binding domain were of the CSH module modelled as Mg.ADP and the adenosine 3'-phosphate 5'-diphosphate moiety of bound EVT0185-CoA, respectively. Restraints for EVT0185-CoA were generated via de Grade Web Server (https://grade.globalphasing.org).
Data Acquisition
Detector Type GATAN K3 (6k x 4k)
Electron Dose (electrons/Å2) 61.8
Imaging Experiment
Date of Experiment ?
Temprature (Kelvin)
Microscope Model JEOL CRYO ARM 300
Minimum Defocus (nm) 1200
Maximum Defocus (nm) 1800
Minimum Tilt Angle (degrees) ?
Maximum Tilt Angle (degrees) ?
Nominal CS ?
Imaging Mode BRIGHT FIELD
Specimen Holder Model JEOL CRYOSPECPORTER
Nominal Magnification ?
Calibrated Magnification ?
Source FIELD EMISSION GUN
Acceleration Voltage (kV) 300
Imaging Details ?
Imaging Experiment
Task Software Package Version
PARTICLE SELECTION cryoSPARC v3.1.0
IMAGE ACQUISITION SerialEM ?
CTF CORRECTION cryoSPARC v3.1.0
MODEL FITTING UCSF Chimera 1.17
MODEL REFINEMENT PHENIX 1.20.1
INITIAL EULER ASSIGNMENT cryoSPARC v3.1.0
FINAL EULER ASSIGNMENT cryoSPARC v3.1.0
CLASSIFICATION cryoSPARC v3.1.0
RECONSTRUCTION cryoSPARC v3.1.0
Image Processing
CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION ?
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