5OYB
Structure of calcium-bound mTMEM16A chloride channel at 3.75 A resolution
ELECTRON MICROSCOPY
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 31.371 |
| r_dihedral_angle_3_deg | 14.612 |
| r_long_range_B_refined | 13.657 |
| r_long_range_B_other | 13.656 |
| r_dihedral_angle_4_deg | 12.538 |
| r_mcangle_it | 7.977 |
| r_mcangle_other | 7.977 |
| r_scangle_other | 7.564 |
| r_dihedral_angle_1_deg | 6.212 |
| r_mcbond_it | 4.348 |
| Sample |
|---|
| mTMEM16A with calcium ions bound |
| Specimen Preparation | |
|---|---|
| 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 | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 147368 |
| Reported Resolution (Å) | 3.75 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C2 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 | ||||
| Refinement Space | |||||
| Refinement Protocol | RIGID BODY FIT | ||||
| Refinement Target | |||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K2 SUMMIT (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 80 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TITAN KRIOS |
| Minimum Defocus (nm) | 500 |
| Maximum Defocus (nm) | 3000 |
| 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 | 46511 |
| Calibrated Magnification | 46511 |
| 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 | |
| INITIAL EULER ASSIGNMENT | RELION | 21b1 |
| FINAL EULER ASSIGNMENT | RELION | 2.1b1 |
| CLASSIFICATION | RELION | 2.1b1 |
| RECONSTRUCTION | RELION | 2.1b1 |
| MODEL REFINEMENT | PHENIX | |
| MODEL REFINEMENT | REFMAC | 5 |
| Image Processing | ||||
|---|---|---|---|---|
| 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 | 629679 | For the dataset collected in presence of calcium ions a total of 4,342 dose-fractionated super-resolution images were recorded, 2 x 2 down-sampled by Fourier cropping (final pixel size 1.075A) and subjected to motion correction and dose-weighting of frames by MotionCor248. The contrast transfer function (CTF) parameters were estimated on the movie frames by ctffind4.149. Images showing a strong drift, higher defocus than -3.0 um or a bad CTF estimation were discarded, resulting in 2,997 images used for further analysis with the software package RELION2.1b150. Particles were picked automatically using 2D class averages from the previously obtained TMEM16A cryo-EM map as reference26 providing an initial set of 629,679 particles. After extraction with a box size of 300 pixels, false positives were eliminated manually or through a first round of 2D classification, resulting in 368,162 particles that were further subjected to several rounds of 2D classification to remove particles belonging to low-abundance classes. The remaining 252,577 particles were sorted during 3D Classification, a C2 symmetry was imposed and the low-resolution TMEM16A cryo-EM map (EMD-3658) was used as initial model. The best class, comprising 147,368 particles from a total of 2012 images, was subjected to auto-refinement and particle polishing in RELION, with a running average window of 5, a standard deviation of 1 pixel on translations and 200 pixels on particle distance. The final polished and auto-refined map used for model building had a resolution of 4.6A before masking and 3.75A after masking and was sharpened using an isotropic b-factor of -1063A2 | |
