8RQ5
Cryo-EM structure of the light-driven sodium-pumping rhodopsin KR2
ELECTRON MICROSCOPY
Refinement
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_3_deg | 14.413 |
r_long_range_B_refined | 10.211 |
r_long_range_B_other | 10.211 |
r_scangle_other | 8.715 |
r_dihedral_angle_2_deg | 8.53 |
r_mcangle_it | 5.686 |
r_mcangle_other | 5.686 |
r_scbond_it | 5.644 |
r_scbond_other | 5.644 |
r_dihedral_angle_1_deg | 5.028 |
Sample |
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Sodium-pumping rhodopsin |
Specimen Preparation | |
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Sample Aggregation State | PARTICLE |
Vitrification Instrument | |
Cryogen Name | ETHANE |
Sample Vitrification Details | Jet vitrified with EasyGrid |
3D Reconstruction | |
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Reconstruction Method | SINGLE PARTICLE |
Number of Particles | 333078 |
Reported Resolution (Å) | 2.32 |
Resolution Method | FSC 0.143 CUT-OFF |
Other Details | |
Refinement Type | |
Symmetry Type | POINT |
Point Symmetry | C5 |
Map-Model Fitting and Refinement | |||||
---|---|---|---|---|---|
Id | 1 | ||||
Refinement Space | REAL | ||||
Refinement Protocol | RIGID BODY FIT | ||||
Refinement Target | |||||
Overall B Value | |||||
Fitting Procedure | |||||
Details |
Data Acquisition | |||||||||
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Detector Type | GATAN K3 (6k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 40.3 |
Imaging Experiment | 1 |
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Date of Experiment | |
Temperature (Kelvin) | |
Microscope Model | FEI TITAN KRIOS |
Minimum Defocus (nm) | 800 |
Maximum Defocus (nm) | 2400 |
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 | 105000 |
Calibrated Magnification | |
Source | FIELD EMISSION GUN |
Acceleration Voltage (kV) | 300 |
Imaging Details |
EM Software | ||
---|---|---|
Task | Software Package | Version |
PARTICLE SELECTION | cryoSPARC | 4.2 |
IMAGE ACQUISITION | EPU | |
CTF CORRECTION | cryoSPARC | 4.2 |
INITIAL EULER ASSIGNMENT | cryoSPARC | 4.2 |
FINAL EULER ASSIGNMENT | cryoSPARC | 4.2 |
CLASSIFICATION | cryoSPARC | 4.2 |
RECONSTRUCTION | cryoSPARC | 4.2 |
Image Processing | ||||
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CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
PHASE FLIPPING AND AMPLITUDE CORRECTION | 1916000 | A first round of blob picking was performed and used to obtain an initial model. this initial model was used to generate templates that were then used to performed template picking, resulting in 1916000 particles |