9FJM
Cryo-EM structure of the phalloidin-bound pointed end of the actin filament.
ELECTRON MICROSCOPY
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 8RTT |
Refinement
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 7.368 |
f_angle_d | 0.552 |
f_chiral_restr | 0.042 |
f_plane_restr | 0.004 |
f_bond_d | 0.002 |
Sample |
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Actin filament pointed end bound by phalloidin |
Sample Components |
Actin filament pointed end |
Phalloidin |
Specimen Preparation | |
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Sample Aggregation State | PARTICLE |
Vitrification Instrument | FEI VITROBOT MARK IV |
Cryogen Name | ETHANE-PROPANE |
Sample Vitrification Details | 3 seconds, force 0. |
3D Reconstruction | |
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Reconstruction Method | SINGLE PARTICLE |
Number of Particles | 280802 |
Reported Resolution (Å) | 3.65 |
Resolution Method | FSC 0.143 CUT-OFF |
Other Details | Local Refinement in CryoSPARC. |
Refinement Type | |
Symmetry Type | POINT |
Point Symmetry | C1 |
Map-Model Fitting and Refinement | |||||
---|---|---|---|---|---|
Id | 1 (8rtt) | ||||
Refinement Space | REAL | ||||
Refinement Protocol | FLEXIBLE FIT | ||||
Refinement Target | |||||
Overall B Value | |||||
Fitting Procedure | |||||
Details |
Data Acquisition | |||||||||
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Detector Type | GATAN K3 BIOQUANTUM (6k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 64.6 |
Imaging Experiment | 1 |
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Date of Experiment | |
Temperature (Kelvin) | |
Microscope Model | FEI TITAN KRIOS |
Minimum Defocus (nm) | 1200 |
Maximum Defocus (nm) | 2700 |
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 | 81000 |
Calibrated Magnification | |
Source | FIELD EMISSION GUN |
Acceleration Voltage (kV) | 300 |
Imaging Details | 300 kV Titan Krios G2 microscope (Thermo Fisher Scientific) with an in-column Cs-corrector. |
EM Software | ||
---|---|---|
Task | Software Package | Version |
PARTICLE SELECTION | crYOLO | 1.5.8 |
IMAGE ACQUISITION | EPU | |
CTF CORRECTION | CTFFIND | 4.13 |
MODEL FITTING | UCSF ChimeraX | 1.5 |
MODEL FITTING | Coot | 0.9.8.1 |
INITIAL EULER ASSIGNMENT | cryoSPARC | v3.3.2 |
FINAL EULER ASSIGNMENT | cryoSPARC | v4.0.3 |
CLASSIFICATION | cryoSPARC | v4.2.1 |
RECONSTRUCTION | cryoSPARC | v4.2.1 |
MODEL REFINEMENT | Coot | 0.9.8.1 |
MODEL REFINEMENT | PHENIX | 1.21rc1_5015 |
Image Processing | ||||
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CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
PHASE FLIPPING AND AMPLITUDE CORRECTION | 5200600 | Particles picked using SPHIRE-crYOLO. |