6X8T
CryoEM structure of the apo-SrpI encapasulin complex from Synechococcus elongatus PCC 7942
ELECTRON MICROSCOPY
Refinement
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 17.865 |
f_angle_d | 0.663 |
f_chiral_restr | 0.05 |
f_bond_d | 0.007 |
f_plane_restr | 0.006 |
Sample |
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SrpI encapsulin apo complex |
Specimen Preparation | |
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Sample Aggregation State | PARTICLE |
Vitrification Instrument | FEI VITROBOT MARK IV |
Cryogen Name | ETHANE |
Sample Vitrification Details | blot force 5, 3 sec blot, 100 humidity, 4C, 1 sec drain time |
3D Reconstruction | |
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Reconstruction Method | SINGLE PARTICLE |
Number of Particles | 34425 |
Reported Resolution (Å) | 2.9 |
Resolution Method | FSC 0.143 CUT-OFF |
Other Details | |
Refinement Type | |
Symmetry Type | POINT |
Point Symmetry | I |
Map-Model Fitting and Refinement | |||||
---|---|---|---|---|---|
Id | 1 | ||||
Refinement Space | REAL | ||||
Refinement Protocol | RIGID BODY FIT | ||||
Refinement Target | Correlation coefficient | ||||
Overall B Value | 20 | ||||
Fitting Procedure | |||||
Details | One subunit was built completely de novo based on sequence/density, and iteratively real space refined with neighboring subunits using PHENIX. |
Data Acquisition | |||||||||
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Detector Type | GATAN K3 BIOQUANTUM (6k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 40 |
Imaging Experiment | 1 |
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Date of Experiment | |
Temperature (Kelvin) | |
Microscope Model | FEI TECNAI ARCTICA |
Minimum Defocus (nm) | 1000 |
Maximum Defocus (nm) | 2500 |
Minimum Tilt Angle (degrees) | |
Maximum Tilt Angle (degrees) | |
Nominal CS | 2.6 |
Imaging Mode | BRIGHT FIELD |
Specimen Holder Model | FEI TITAN KRIOS AUTOGRID HOLDER |
Nominal Magnification | 36000 |
Calibrated Magnification | |
Source | FIELD EMISSION GUN |
Acceleration Voltage (kV) | 200 |
Imaging Details | Residual beam tilt corrected in RELION/3.1. CTF refinement performed in RELION/3.1. |
EM Software | ||
---|---|---|
Task | Software Package | Version |
PARTICLE SELECTION | RELION | 3.1 |
IMAGE ACQUISITION | SerialEM | |
CTF CORRECTION | CTFFIND | 4.1.10 |
MODEL FITTING | PHENIX | 1.18_3845 |
INITIAL EULER ASSIGNMENT | RELION | 3.1 |
FINAL EULER ASSIGNMENT | RELION | 3.1 |
RECONSTRUCTION | RELION | 3.1 |
MODEL REFINEMENT | PHENIX | 1.18_3845 |
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 refinement was performed in Relion/3.1 | 57431 | Relion LoG autopicker to select particles |