REL RCSB RCSB RCSB 2014-08-12 2014-09-24 2014-10-15 2014-11-19 Guo F Liu Z Fang PA Zhang Q Wright ET Wu W Zhang C Vago F Ren Y Jakata J Chiu W Serwer P Jiang W Bacteriophage T7, Maturation, DNA packaging, Procapsid, Non-covalent topological linking, Single particle cryo-EM Guo F Liu Z Fang PA Zhang Q Wright ET Wu W Zhang C Vago F Ren Y Jakata J Chiu W Serwer P Jiang W PROC.NAT.ACAD.SCI.USA 111 e4606 e4614 2014 25313071 doi:10.1073/pnas.1407020111 3j7x FULLOVERLAP Bacteriophage T7 mature phage capsid Bacteriophage T7 mature phage capsid 415 copies of gp10A form T=7 icosahedral shell 1 15.1 Enterobacteria phage T7 Enterobacteria phage T7 Escherichia coli BACTERIA(EUBACTERIA) 15.1 mature phage capsid 564 7 VIRION SPECIES false false singleParticle particle 7.4

200 mM NaCl, 10 mM Tris-HCl, 1 mM MgCl2

400 mesh copper grid with one lacy carbon layer

ETHANE 90 120 FEI VITROBOT MARK I Blot for 2 seconds twice with 2 mm offset before plunging. FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 0.6 2.4 59000.0 57727.0 FEI TITAN KRIOS AUTOGRID HOLDER 80 100 95 2010-08-09 KODAK SO-163 FILM NIKON SUPER COOLSCAN 9000 6.35 364 25 1.0 16. Liquid nitrogen-cooled

Particles were selected from scanned micrograph images, first automatically by the ethan method and then by manual screening with the boxer program in EMAN. The TEM instrument contrast transfer function parameters were determined automatically using fitctf2.py and were then visually validated using the EMAN ctfit program. The datasets were then divided into two subsets (even and odd) and processed completely independently, including both initial models and refinements. For 3D reconstructions, the whole datasets were divided into even-odd halves and the initial de novo models and subsequent iterative refinements were all independently performed for each half dataset. The images were first binned 4x to obtain initial models and particle parameters assuming icosahedral symmetry. De novo initial models were built using the random model approach. Random subsets of particles were assigned random initial orientations and iteratively refined until convergence. Consistent icosahedral capsid structures (other than occasional differences in handedness) were obtained by repeating the random model process. Particles with inconsistent/unstable view parameters in the initial refinements were excluded in further image processing. The orientation and center parameters were then transferred to the un-binned images for high-resolution refinements which included Simplex method-based orientation/center optimization and grid search-based refinement of defocus, astigmatism, and magnification of the images. All image refinement and reconstructions were performed with in-house developed programs jspr.py (for overall work-flow), jalign (for 2D alignment) and j3dr (for 3D reconstruction), which use EMAN and EMAN2 library functions.

Each particle

OTHER 3.6 OTHER jspr, EMAN, EMAN2

For 3D reconstruction, whole datasets were divided into even and odd halves and the initial de novo models and subsequent iterative refinements were all independently performed for each half dataset.

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