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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
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
r_mcbond_other
4.347
r_scbond_it
4.113
r_scbond_other
4.113
r_angle_other_deg
3.646
r_angle_refined_deg
1.277
r_chiral_restr
0.107
r_bond_refined_d
0.007
r_gen_planes_refined
0.006
r_gen_planes_other
0.004
r_bond_other_d
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
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