ELECTRON MICROSCOPY

Sample

BMOE-crosslinked complex of Gb1g2 and PLCb3

Specimen Preperation
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 65306
Reported Resolution (Å) 7
Resolution Method FSC 0.143 CUT-OFF
Other Details ?
Refinement Type
Symmetry Type POINT
Map-Model Fitting and Refinement
ID 1
Refinement Space ?
Refinement Protocol FLEXIBLE FIT
Refinement Target ?
Overall B Value ?
Fitting Procedure ?
Details Crystal structures of Gbetagamma and PLCbeta3 (PDB IDs 1GP2 and 4GNK) were rigid-body fit into the cryo-EM map using Chimera. The model was refined using molecular dynamic flexible fitting (MDFF). MDFF configuration files were generated using VMD. During MDFF simulation, Gbetagamma was set as rigid with domain restraints. The MDFF simulation was conducted with a grid scaling value of 0.5 for 100 ps, followed by 3,000 steps of energy minimization until convergence of the protein RMSD. The MDFF generated model was inspected and manually adjusted in Coot, guided through the use of deep-learning-based amino-acid-wise model quality (DAQ) scoring, and refined in PHENIX.
Data Acquisition
Detector Type GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å2) 53.69
Imaging Experiment
Date of Experiment ?
Temprature (Kelvin)
Microscope Model TFS KRIOS
Minimum Defocus (nm) 1000
Maximum Defocus (nm) 3000
Minimum Tilt Angle (degrees) ?
Maximum Tilt Angle (degrees) ?
Nominal CS ?
Imaging Mode BRIGHT FIELD
Specimen Holder Model ?
Nominal Magnification ?
Calibrated Magnification ?
Source FIELD EMISSION GUN
Acceleration Voltage (kV) 300
Imaging Details ?
Imaging Experiment
Task Software Package Version
PARTICLE SELECTION cryoSPARC ?
IMAGE ACQUISITION Leginon ?
CTF CORRECTION CTFFIND ?
MODEL FITTING UCSF Chimera ?
MODEL FITTING MDFF ?
FINAL EULER ASSIGNMENT cryoSPARC ?
RECONSTRUCTION Coot ?
RECONSTRUCTION PHENIX ?
MODEL REFINEMENT PHENIX 1.21.2_5419
Image Processing
CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION ?
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