7LRE
Cryo-EM of the SLFN12-PDE3A complex: SLFN12 body refinement
ELECTRON MICROSCOPY
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5YD0 |
Refinement
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 7.4095 |
f_angle_d | 0.4396 |
f_chiral_restr | 0.0401 |
f_bond_d | 0.0025 |
f_plane_restr | 0.0025 |
Sample |
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SLFN12-PDE3A complex, SLFN12 body |
Specimen Preparation | |
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Sample Aggregation State | PARTICLE |
Vitrification Instrument | FEI VITROBOT MARK IV |
Cryogen Name | ETHANE |
Sample Vitrification Details | 4.5 second blot time |
3D Reconstruction | |
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Reconstruction Method | SINGLE PARTICLE |
Number of Particles | 247402 |
Reported Resolution (Å) | 2.76 |
Resolution Method | FSC 0.143 CUT-OFF |
Other Details | Multi-body refinement in Relion |
Refinement Type | |
Symmetry Type | POINT |
Point Symmetry | C2 |
Map-Model Fitting and Refinement | |||||
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Id | 1 (5YD0) | ||||
Refinement Space | REAL | ||||
Refinement Protocol | |||||
Refinement Target | |||||
Overall B Value | |||||
Fitting Procedure | |||||
Details | The atomic model (including per-residue ADP/B-factors) was refined in Phenix against the sharpened/local resolution-filtered map |
Data Acquisition | |||||||||
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Detector Type | GATAN K3 BIOQUANTUM (6k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 50 |
Imaging Experiment | 1 |
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Date of Experiment | |
Temperature (Kelvin) | |
Microscope Model | FEI TITAN KRIOS |
Minimum Defocus (nm) | |
Maximum Defocus (nm) | |
Minimum Tilt Angle (degrees) | |
Maximum Tilt Angle (degrees) | |
Nominal CS | 2.7 |
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 |
EM Software | ||
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Task | Software Package | Version |
IMAGE ACQUISITION | EPU | 2.5 |
CTF CORRECTION | CTFFIND | 4.1.13 |
INITIAL EULER ASSIGNMENT | cisTEM | 1.0.0-beta |
FINAL EULER ASSIGNMENT | RELION | 3.1 |
CLASSIFICATION | RELION | 3.1 |
RECONSTRUCTION | RELION | 3.1 |
MODEL REFINEMENT | PHENIX | 1.18 |
MODEL REFINEMENT | Coot | 0.8.9 |
Image Processing | ||||
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CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
PHASE FLIPPING AND AMPLITUDE CORRECTION | CTF correction was applied throughout the entire processing workflow, beginning with particle picking | 2160426 |