ELECTRON MICROSCOPY
Refinement
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 3.639 |
f_angle_d | 0.475 |
f_chiral_restr | 0.039 |
f_plane_restr | 0.006 |
f_bond_d | 0.004 |
Sample |
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Cryo-EM structure of the pentameric human MRS2 magnesium channel under Mg2+ condition at an average resolution of 2.8 A, filtered to local resolution, C5 |
Specimen Preparation | |
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Sample Aggregation State | PARTICLE |
Vitrification Instrument | LEICA EM GP |
Cryogen Name | ETHANE |
Sample Vitrification Details | 400-mesh R1.2/1.3 Cu grids (Quantifoil) were made hydrophilic by glow discharging for 60 seconds with a current of 15 mA in a PELCO easiGlow system. T ... |
3D Reconstruction | |
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Reconstruction Method | SINGLE PARTICLE |
Number of Particles | 450554 |
Reported Resolution (Å) | 2.8 |
Resolution Method | FSC 0.143 CUT-OFF |
Other Details | Non-uniform refinement was performed with 450,554 selected particles, followed by local motion correction and CTF refinement to correct for beam-tilt, ... |
Refinement Type | |
Symmetry Type | POINT |
Point Symmetry | C5 |
Map-Model Fitting and Refinement | |||||
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Id | 1 | 2 | |||
Refinement Space | REAL | REAL | |||
Refinement Protocol | RIGID BODY FIT | FLEXIBLE FIT | |||
Refinement Target | |||||
Overall B Value | 141 | 141 | |||
Fitting Procedure | |||||
Details | The model was then manually rebuilt in COOT v.0.9.7 using the local resolution filtered map, which was generated from refinement with C5 applied. The ... |
Data Acquisition | |||||||||
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Detector Type | GATAN K3 BIOQUANTUM (6k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 50 |
Imaging Experiment | 1 |
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Date of Experiment | |
Temperature (Kelvin) | |
Microscope Model | FEI TITAN KRIOS |
Minimum Defocus (nm) | 700 |
Maximum Defocus (nm) | 2000 |
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 | ||
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Task | Software Package | Version |
PARTICLE SELECTION | cryoSPARC | 3.3.2 |
IMAGE ACQUISITION | SerialEM | |
CTF CORRECTION | cryoSPARC | 3.3.2 |
MODEL FITTING | UCSF Chimera | 1.16 |
INITIAL EULER ASSIGNMENT | cryoSPARC | 3.3.2 |
FINAL EULER ASSIGNMENT | cryoSPARC | 3.3.2 |
CLASSIFICATION | cryoSPARC | 3.3.2 |
RECONSTRUCTION | cryoSPARC | 3.3.2 |
MODEL FITTING | Coot | |
MODEL REFINEMENT | Coot | |
MODEL REFINEMENT | PHENIX | 1.20.1-4487 |
Image Processing | ||||
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CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
PHASE FLIPPING AND AMPLITUDE CORRECTION | Patch CTF | 1568444 | Good 2D class averages generated from ~1,000 manually picked particles served as templates for automatic particle picking. |