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Tetra-phosphorylated, E1435Q Ycf1 mutant in inward-facing wide conformation
ELECTRON MICROSCOPY
Starting Model(s)
Initial Refinement Model(s)
Type
Source
Accession Code
Details
in silico model
AlphaFold
p39109
Refinement
RMS Deviations
Key
Refinement Restraint Deviation
f_dihedral_angle_d
11.32
f_angle_d
0.588
f_chiral_restr
0.039
f_bond_d
0.004
f_plane_restr
0.004
Sample
Phosphorylated, E1435Q Ycf1 mutant in inward-facing wide conformation
Specimen Preparation
Sample Aggregation State
PARTICLE
Vitrification Instrument
LEICA EM GP
Cryogen Name
ETHANE
Sample Vitrification Details
5 microliters of sample of concentrated E1435Q (5.94 mg/mL) PKA-treated Ycf1 sample was applied to QF-1.2/1,3 Au grid. Grids were place inside of a Le ...
5 microliters of sample of concentrated E1435Q (5.94 mg/mL) PKA-treated Ycf1 sample was applied to QF-1.2/1,3 Au grid. Grids were place inside of a Leica EM GP2 equilibrated at 10 degress Celcius amd 80% humidity. Following 10 seconds incubation, the side of the grid to which the sample was applied was blotted on a Whatman 1 paper (3.5 seconds) then immediately plunge frrozen in liquid ethan equilibrated at -185 degree Celcius.
3D Reconstruction
Reconstruction Method
SINGLE PARTICLE
Number of Particles
68169
Reported Resolution (Å)
3.23
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
AB INITIO MODEL
Refinement Target
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector Type
GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)
54
Imaging Experiment
1
Date of Experiment
Temperature (Kelvin)
Microscope Model
TFS KRIOS
Minimum Defocus (nm)
900
Maximum Defocus (nm)
2100
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging Mode
BRIGHT FIELD
Specimen Holder Model
Nominal Magnification
Calibrated Magnification
Source
FIELD EMISSION GUN
Acceleration Voltage (kV)
300
Imaging Details
EM Software
Task
Software Package
Version
PARTICLE SELECTION
cryoSPARC
4.2.1
IMAGE ACQUISITION
cryoSPARC
CTF CORRECTION
cryoSPARC
4.2.1
MODEL FITTING
ISOLDE
1.3
MODEL REFINEMENT
PHENIX
1.20.1
RECONSTRUCTION
cryoSPARC
4.2.1
Image Processing
CTF Correction Type
CTF Correction Details
Number of Particles Selected
Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION
4840688
Manual and auto particle picking and extraction from 8380 curated micropgrahs