4AQ9 | pdb_00004aq9

Gating movement in acetylcholine receptor analysed by time- resolved electron cryo-microscopy (open class)

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2BG9

Sample
NICOTINIC ACETYLCHOLINE RECEPTOR IN NATIVE POSTSYNAPTIC MEMBRANE FROM TORPEDO MARMORATA

Specimen Preparation
Sample Aggregation State	HELICAL ARRAY
Vitrification Instrument	HOMEMADE PLUNGER
Cryogen Name	ETHANE
Sample Vitrification Details	VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 85 TEMPERATURE- 120 INSTRUMENT- HOMEMADE PLUNGER METHOD- BLOT UNTIL APPLIED DROPLET LOSES CONTACT WITH F ...	VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 85 TEMPERATURE- 120 INSTRUMENT- HOMEMADE PLUNGER METHOD- BLOT UNTIL APPLIED DROPLET LOSES CONTACT WITH FILTER PAPER (INDICATED BY LOSS OF TRANSPARENCY TYPICALLY 6S) TIMERESOLVEDSTATE- VITRIFIED WITHIN 10MS OF EXPOSURE TO ACETYLCHOLINE (APPLIED AS THE GRID IS BEING PLUNGED USING A FINE FOCUSSED SPRAY POSITIONED ABOUT 1CM ABOVE THE ETHANE SURFACE) DETAILS- VITRIFICATION CARRIED OUT AT AN AMBIENT TEMPERATURE OF 8 DEGREES

3D Reconstruction
Reconstruction Method	HELICAL
Number of Particles
Reported Resolution (Å)	6.2
Resolution Method
Other Details	FOURIER-BESSEL SYNTHESIS AFTER APPLYING DISTORTION CORRECTIONS TO THE IMAGES SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2072.
Refinement Type
Symmetry Type	HELICAL

Map-Model Fitting and Refinement
Id	1 (2BG9)
Refinement Space	REAL
Refinement Protocol	FLEXIBLE FIT
Refinement Target
Overall B Value
Fitting Procedure
Details	METHOD--MAXIMISATION OF CORRELATION BETWEEN EXPERIMENTAL DENSITIES AND ATOMIC MODEL, USING A DEFORMABLE ELASTIC NETWORK ALGORITHM (DIREX) REFINEMENT ...	METHOD--MAXIMISATION OF CORRELATION BETWEEN EXPERIMENTAL DENSITIES AND ATOMIC MODEL, USING A DEFORMABLE ELASTIC NETWORK ALGORITHM (DIREX) REFINEMENT PROTOCOL--LOW RESOLUTION X-RAY

Data Acquisition
Detector Type	KODAK SO-163 FILM
Electron Dose (electrons/Å**2)	25

Imaging Experiment	1
Date of Experiment	2005-11-01
Temperature (Kelvin)	4
Microscope Model	JEOL 3000SFF
Minimum Defocus (nm)	900
Maximum Defocus (nm)	2000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	1.6
Imaging Mode	BRIGHT FIELD
Specimen Holder Model
Nominal Magnification	40000
Calibrated Magnification	38500
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details	STANDARD LOW DOSE IMAGING OF SPECIMENS OVER HOLES IN THE CARBON SUPPORT FILM

EM Software
Task	Software Package	Version
MODEL FITTING	DireX
RECONSTRUCTION	Custom
RECONSTRUCTION	MRC IMAGE PROCESSING PACKAGE

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
	EACH TUBE IMAGE

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.