REL RCSB RCSB RCSB 2014-06-24 2014-07-30 2014-07-30 2015-10-07 Bartesaghi A Matthies D Banerjee S Merk A Subramaniam S atomic resolution cryo-electron microscopy, single-particle EM, direct electron detectors, 3D reconstruction, frame alignment, CTF determination, structure refinement, radiation damage, protein complexes, enzyme active site structure Bartesaghi A Matthies D Banerjee S Merk A Subramaniam S PROC.NAT.ACAD.SCI.USA 111 11709 11714 2014 25071206 doi:10.1073/pnas.1402809111 3j7h FULLOVERLAP http://dx.doi.org/10.6019/EMPIAR-10013 Escherichia coli beta-galactosidase Escherichia coli beta-galactosidase

The sample was monodisperse.

tetramer 1 0.465 ProtParam tool: Gasteiger E., Hoogland C., Gattiker A., Duvaud S., Wilkins M.R., Appel R.D., Bairoch A., Protein Identification and Analysis Tools on the ExPASy Server, (in) John M. Walker (ed): The Proteomics Protocols Handbook, Humana Press (2005), pp. 571-607 beta-galactosidase Escherichia coli K-12 cytoplasm 0.465 1 tetramer false P00722 GO:0004565 singleParticle particle 2.3 8.0

25 mM Tris, pH 8.0, 50 mM NaCl, 2 mM MgCl2, 0.5 mM TCEP

200 mesh Quantifoil R2/2 grids, plasma cleaned

ETHANE 90 90.15 LEICA EM GP Blot for 2 seconds before plunging. FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 1.0 2.5 105000.0 105000.0 FEI TITAN KRIOS AUTOGRID HOLDER 79.6 79.8 79.7 Objective lens astigmatism was corrected at 105,000 times magnification. 5 Gatan, Inc. 0.0 20.0

Parallel beam illumination

2013-10-31 GATAN K2 (4k x 4k) 509 45

Every image is the average of 38 frames recorded by the direct electron detector. The complete set of electron micrographs used to obtain the density map presented here is available through the Electron Microscopy Pilot Image ARchive (EMPIAR).

Liquid nitrogen cooled

Individual frames of each movie were aligned by cross-correlation using the cumulative average of previously aligned frames as a reference to align the remaining frames. Parameters of the contrast transfer function for each micrograph were estimated from power spectra obtained using periodogram averaging with tiles of size 512x512 pixels extracted from all frames of each movie. These power spectra were then radially averaged and used to estimate the defocus for each image using frequencies in the 15.0-3.0 Angstrom range. 24,750 particles were picked automatically from the best 509 micrographs by detecting the local maxima of correlation of each image with a Gaussian disk of 100 Angstrom in radius and extracted using a binning factor of 2 and a box size of 384x384 pixels. Particles were then subjected to reference-free 2D classification in EMAN2. 160 classes out of a total of 250 were used for de novo initial model determination using e2initialmodel.py and imposing D2 symmetry. A subset of 23,452 particles (corresponding to the 160 classes used for the initial model building) was then used for 3D refinement using a gold-standard approach. Two stacks of 11,726 particles each were independently subjected to eight rounds of iterative refinement in FREALIGN using a high-resolution frequency limit of 8 Angstrom and using the best 50% of particles from each stack according to phase residual values (equivalent to 5,863 particles) to calculate the reconstructions at each iteration. At this point particles were re-extracted from the original unbinned micrographs using a box size of 768x768 pixels and further refined in FREALIGN starting from the most recent set of alignments obtained with the binned data. The final map was obtained by averaging the two half-reconstructions in real space and corrected by a B-factor of -85 Angstrom^2 for the purpose of visualization.

each particle

OTHER 3.2 OTHER FREALIGN, EMAN2 11726 emd_5995_fsc.xml