5OYG | pdb_00005oyg

Structure of calcium-free mTMEM16A chloride channel at 4.06 A resolution

ELECTRON MICROSCOPY

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Refinement

RMS Deviations
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
r_scbond_other	5.664
r_mcbond_it	5.315
r_mcbond_other	5.314
r_angle_other_deg	3.701
r_angle_refined_deg	1.295
r_chiral_restr	0.105
r_bond_refined_d	0.007
r_gen_planes_refined	0.005
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 in absence of calcium ions

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	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
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)	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
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