REL RCSB RCSB RCSB 2015-12-07 2016-02-03 2016-02-03 2016-03-30 Liu Z Guo F Wang F Li TC Jiang W de novo initial model, consensus criterion, gold-standard FSC, true FSC, cross-validation Liu Z Guo F Wang F Li TC Jiang W STRUCTURE 24 319 328 2016 26777413 doi:10.1016/j.str.2015.12.006 3jci FULLOVERLAP Porcine circovirus PCV2 virus-like particles Porcine circovirus PCV2 virus-like particles 1 1.67 1.67 Porcine circovirus 2 Porcine circovirus 2 Yamagata Sus scrofa VERTEBRATES Trichoplusia ni Tn5 AcPCV2-ORF2 1.67 1.67 190 1 VIRUS-LIKE PARTICLE STRAIN false true PCV2 singleParticle particle 3 7.4

1x PBS

400-mesh holey carbon grids (1.2/1.3 C-flat, Protochips)

ETHANE 90 85 GATAN CRYOPLUNGE 3 Blot for 5 seconds before plunging. FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 0.2 2.5 59000.0 FEI TITAN KRIOS AUTOGRID HOLDER 80 100 90 Objective lens astigmatism was corrected at 250,000 magnification using a quadrupole stigmator. 2011-02-22 KODAK SO-163 FILM NIKON SUPER COOLSCAN 9000 6.35 141 25 1.0 16.

The particles were selected using the e2boxer.py program in EMAN2. CTF parameters were determined using fitctf2.py in JSPR.

Each particle

OTHER 2.9 OTHER JSPR, 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. Particles were selected from scanned micrograph images using e2boxer.py in EMAN2. The TEM instrument contrast transfer function parameters were determined automatically using fitctf2.py in JSPR 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 de novo initial models and refinements. 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. Multi-model competitive refinements were used to choose the winning model (with most assigned particles) as corrective initial models for subsequent refinement. 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, beam tilt, and overall and anisotropic magnification of the images. All image refinement and reconstructions were performed with JSPR software that was built on EMAN2 and EMAN library functions and programs.

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