Ab initio model datasets of 50S ribosomal subunit¶

Information¶

These datasets were used to support various Ab initio reconstruction procedures as described in (Voss et al. 2010).

The experiments included are: YYmonDDa etc., where YY refers to the year, mon to the month and DD to the day of data acquisition. a, b, c, etc. are subsequent experiments on that day.

Original images may be viewed using the Leginon image viewer and downloaded one-by-one from the Leginon viewer or as an entire set using the dbemwiz.jar tool and selecting the experiment, named as YYmonDDa.
Summary information may be viewed using the Leginon summary pages and processed data may be examined using the Appion processing pipeline. Images and metadata may be downloaded from these websites or using the links below.

List of available datasets:¶

Session Name	Leginon Description
09apr14b	50S Ribosome subunit, vitreous ice, 100k particles
09mar04b	50S Ribosome subunit, vitreous ice, Pt Coated C_Flats
09feb18c	50S Ribosome subunit, tomography
09feb12b	50S Ribosomesubunit, RCT data

Download Raw Stacks¶

Note: all stacks have been CTF corrected using a Weiner filter with ACE2, a variation of the ACE1 algorithm described in Mallick el al., 2005

Name	IMAGIC .hed file	IMAGIC .img file
Projection-matching refinement stack	start.hed	start.img
Common lines stack	start.hed	start.img
Untilted random conical tilt (RCT) stack	start.hed	start.img
Tilted random conical tilt (RCT) stack	start.hed	start.img
Synthetic 50S projections stack	ctfstack_snr0.05.hed	ctfstack_snr0.05.img

Download Tomography tilt series stack and tilts¶

The tilt stack file is a 32-bit real mrc file without extended header. Combined with the information in the tilt angle (.rawtilt) file, it can be used in most tomography packages.

Name	rawtilt text file	tiltstack mrc file
Tilt series 6	09feb18c_006.rawtlt	09feb18c_006.st

Download initial models and final reconstructions¶

Note: Refinement was done using the EMAN1 refine program for 12 iterations. Final reconstruction are the raw volume from EMAN, no amplitude correction has been performed.

Name	Initial model	Final reconstruction
Ab initio models
PDB structure	download model	download density
EMDB structure	download model	download density
Angular reconstitution	download model	download density
Cross-common lines (improved class averages)	download model	download density
Random conical tilt (RCT)	download model	download density
Sub-tomogram averaging	download model	download density
Poor models
Hemisphere	download model	download density
Symmetric Gaussian sphere	download model	download density
Asymmetric Gaussian sphere	download model	download density
Angular reconstitution (poor class averages)	download model	download density
Cross-common lines (poor class averages)	download model	download density

Reference¶

Voss, Lyumkis, Cheng, et al. (2010)
_A toolbox for ab initio 3-D reconstructions in single-particle electron microscopy._
J Struct Biol. v169(3): pp. 389-98.