ELECTRON MICROSCOPY

Sample

YiiP dimer in an inward-facing conformation

Specimen Preperation
Sample Aggregation State HELICAL ARRAY
Vitrification Instrument HOMEMADE PLUNGER
Cryogen Name ETHANE
Sample Vitrification Details ?
3D Reconstruction
Reconstruction Method HELICAL
Number of Particles 72333
Reported Resolution (Å) 4.1
Resolution Method FSC 0.143 CUT-OFF
Other Details Reconstruction was achieved using the IHRSR method implemented in RELION 2.0.
Refinement Type
Symmetry Type HELICAL
Map-Model Fitting and Refinement
ID 1
Refinement Space REAL
Refinement Protocol FLEXIBLE FIT
Refinement Target cross-correlation coefficient
Overall B Value ?
Fitting Procedure ?
Details The residues were manually adjusted in COOT relying on the large side-chain residues, and the whole system was further optimized using the real_space_refine algorithm in Phenix to ensure proper fit. The conformation was subjected to 13 rounds of COOT/Phenix refinements.
Data Acquisition
Detector Type GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å2) 70
Imaging Experiment
Date of Experiment ?
Temprature (Kelvin)
Microscope Model FEI TITAN KRIOS
Minimum Defocus (nm) 1200
Maximum Defocus (nm) 2500
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 22500
Calibrated Magnification ?
Source LAB6
Acceleration Voltage (kV) 300
Imaging Details ?
Imaging Experiment
Task Software Package Version
PARTICLE SELECTION SPARX/EMAN2 EMAN2.1
PARTICLE SELECTION RELION 2.0
IMAGE ACQUISITION Leginon ?
CTF CORRECTION CTFFIND 4.1
CTF CORRECTION Gctf 0.50
MODEL FITTING Coot 0.8.6
INITIAL EULER ASSIGNMENT RELION 2.0
FINAL EULER ASSIGNMENT RELION 2.0
CLASSIFICATION RELION 2.0
RECONSTRUCTION RELION 2.0
MODEL REFINEMENT PHENIX 1.11
Image Processing
CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION ?
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