9FJY
Structure of the DNase I- and phalloidin-bound pointed end of F-actin (conformer 2).
ELECTRON MICROSCOPY
Refinement
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 6.485 |
f_angle_d | 0.563 |
f_chiral_restr | 0.044 |
f_plane_restr | 0.003 |
f_bond_d | 0.002 |
Sample |
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F-actin pointed end bound by DNase I and phalloidin. |
Sample Components |
Actin filament pointed end |
Phalloidin |
Two DNase I molecules, each bound to the ultimate and penultimate actin subunits of the F-actin pointed end. |
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 | 178346 |
Reported Resolution (Å) | 3.79 |
Resolution Method | FSC 0.143 CUT-OFF |
Other Details | |
Refinement Type | |
Symmetry Type | POINT |
Map-Model Fitting and Refinement | |||||
---|---|---|---|---|---|
Id | 1 (6T20, 2A42) | ||||
Refinement Space | REAL | ||||
Refinement Protocol | FLEXIBLE FIT | ||||
Refinement Target | |||||
Overall B Value | |||||
Fitting Procedure | |||||
Details | Real Space Refinement in Phenix. |
Data Acquisition | |||||||||
---|---|---|---|---|---|---|---|---|---|
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) | 2500 |
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 | 1.8 |
IMAGE ACQUISITION | EPU | |
CTF CORRECTION | CTFFIND | 4.13 |
MODEL FITTING | UCSF ChimeraX | 1.6.1 |
MODEL FITTING | Coot | 0.9.8.1 |
MODEL REFINEMENT | Coot | 0.9.8.1 |
MODEL REFINEMENT | PHENIX | 1.21rc1_5015 |
INITIAL EULER ASSIGNMENT | cryoSPARC | v3.3.2 |
FINAL EULER ASSIGNMENT | cryoSPARC | v4.2.1 |
CLASSIFICATION | cryoSPARC | v4.2.1 |
RECONSTRUCTION | cryoSPARC | v4.2.1 |
Image Processing | ||||
---|---|---|---|---|
CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
PHASE FLIPPING AND AMPLITUDE CORRECTION | 4418492 | Particles picked using SPHIRE-crYOLO. |