5OYG
Structure of calcium-free mTMEM16A chloride channel at 4.06 A resolution
ELECTRON MICROSCOPY
Refinement
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 30.514 |
r_long_range_B_refined | 16.866 |
r_long_range_B_other | 16.865 |
r_dihedral_angle_3_deg | 14.099 |
r_dihedral_angle_4_deg | 13.844 |
r_scangle_other | 10.241 |
r_mcangle_it | 9.597 |
r_mcangle_other | 9.597 |
r_dihedral_angle_1_deg | 6.217 |
r_scbond_it | 5.664 |
Sample |
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mTMEM16A in absence of calcium ions |
Specimen Preparation | |
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Sample Aggregation State | PARTICLE |
Vitrification Instrument | FEI VITROBOT MARK IV |
Cryogen Name | ETHANE |
Sample Vitrification Details | 2 ul sample volume 2-4 sec blotting time |
3D Reconstruction | |
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Reconstruction Method | SINGLE PARTICLE |
Number of Particles | 195465 |
Reported Resolution (Å) | 4.06 |
Resolution Method | FSC 0.143 CUT-OFF |
Other Details | |
Refinement Type | |
Symmetry Type | POINT |
Map-Model Fitting and Refinement | |||||
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Id | 1 | ||||
Refinement Space | |||||
Refinement Protocol | RIGID BODY FIT | ||||
Refinement Target | |||||
Overall B Value | |||||
Fitting Procedure | |||||
Details |
Data Acquisition | |||||||||
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Detector Type | GATAN K2 SUMMIT (4k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 80 |
Imaging Experiment | 1 |
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Date of Experiment | |
Temperature (Kelvin) | |
Microscope Model | FEI TITAN KRIOS |
Minimum Defocus (nm) | 500 |
Maximum Defocus (nm) | 3800 |
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 | 36630 |
Calibrated Magnification | 36630 |
Source | FIELD EMISSION GUN |
Acceleration Voltage (kV) | 300 |
Imaging Details |
EM Software | ||
---|---|---|
Task | Software Package | Version |
PARTICLE SELECTION | RELION | 2.1b1 |
IMAGE ACQUISITION | SerialEM | |
CTF CORRECTION | CTFFIND | 4.1.8 |
MODEL FITTING | Coot | |
MODEL REFINEMENT | PHENIX | |
MODEL REFINEMENT | REFMAC | 5 |
INITIAL EULER ASSIGNMENT | RELION | 21b1 |
FINAL EULER ASSIGNMENT | RELION | 2.1b1 |
CLASSIFICATION | RELION | 2.1b1 |
RECONSTRUCTION | RELION | 2.1b1 |
Image Processing | ||||
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CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
PHASE FLIPPING AND AMPLITUDE CORRECTION | The contrast transfer function (CTF) parameters were estimated on the movie frames by ctffind4.1 | 1349821 | For the dataset collected in absence of calcium ions a total of 5063 dose-fractionated super-resolution images were recorded, 2 x 2 down-sampled by Fourier cropping (final pixel size 1.365A) and subjected to motion correction and dose-weighting of frames by MotionCor2. The contrast transfer function (CTF) parameters were estimated on the movie frames by ctffind4.1. Images showing a strong drift, higher defocus than -3.8 um or a bad CTF estimation were discarded, From a total of 4,738 images (final pixel size 1.365 A) 1,349,821 particles were extracted with a box size of 256 pixels after auto-picking and initial round of 2D classification. Initial rounds of 2D and 3D classification, resulted in a set of 467,286 particles which where subjected to particle polishing, as described above, as well as final rounds of 3D classification. The final polished and auto-refined map was calculated from 195,465 particles derived from 4726 images with a resolution of 4.86 A before masking and 4.06 A after masking and was sharpened using an isotropic b-factor of -116 A2 |