Near-Atomic Resolution of Protein Structure from Electron Cryo-Microscopy
2014 · paper · Instrumentation
Reports the structure of E. coli β-galactosidase at about 3.2-Å resolution using single-particle cryo-electron microscopy. The model closely matches the crystal structure, and negatively charged residues show more radiation damage.
Checked: PDF from europepmc.org, fetched 4 Oct 2026. Page numbers are those of that PDF.
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None that passed a second check.
9 minor (typos and the like; most checked by the judge only)
Wording Page 4: "the pattern of preference for radiation damage is independent of the solvent exposure of the residues (Fig. 5C)" — Fig. 5C plots normalized averaged map values by residue type (buried versus all) from one map and contains no dose comparison.
- p. 4 Left column, first paragraph under Fig. 5
damage is independent of the solvent exposure of the residues
- p. 4 Fig. 5 legend, panel C
Plot of normalized averaged map
Judge's note: Read the text and the Fig. 5 legend and panel C on the page 4 image. Fig. 5C shows hatched (buried) and filled (all) bars of map value per residue type. Radiation damage is offered as the "more likely reason" only in the next paragraph and tested with Fig. 6 and Fig. S12. Fig. 5C supports that the weaker Glu/Asp density is independent of solvent exposure; calling it radiation damage here anticipates the later conclusion. Wording point only.
Second check: another model agreed
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Typo Page 4, discussion: "mammalian TPRV1 channel with regions at 3.4 Å (12)" should read "TRPV1".
- p. 4 Right column, paragraph beginning "In principle"
mammalian TPRV1 channel with regions at 3.4 Å (12)
- p. 4 Right column, same paragraph, later
the TRPV1 channel, where the resolution declines from 3.4 Å
- p. 1 Introduction, last paragraph
reported structure of the TRPV1 channel (12)
- p. 4
mammalian TPRV1 channel with regions at 3.4 Å
Judge's note: The crop C009-a shows "TPRV1". The same channel is spelled TRPV1 on page 1 (line 77), later in the same paragraph (line 348) and in the title of reference 12, and all of these cite reference 12. It is a letter transposition.
Second check: another model agreed
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Typo Page 2, right column: "map derived form the crystal structure (3.6 Å vs. 3.2 Å; Fig. 1B)" should read "derived from".
- p. 2 Results and Discussion, right column, first paragraph
map derived form the crystal structure
- p. 2 Right column, first paragraph
map derived form the crystal structure (3.6 Å vs. 3.2 Å; Fig. 1B)
Judge's note: The page image (crop C001-a) reads "derived form". This is a plain typo for "from".
Second check: another model agreed
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Typo Page 2: "the integrated exposure obtained after alignment of individual frames show well-dispersed particles" — singular subject "exposure" with plural verb "show" (should be "shows").
- p. 2 Left column, first text paragraph under Fig. 1
tegrated exposure obtained after alignment of individual frames
- p. 2 Same sentence, next line
show well-dispersed particles and a variety of distinct views
- p. 2 Results, first paragraph
the integrated exposure obtained after alignment of individual frames show well-dispersed particles
Judge's note: Checked on the page 2 image. "Images were collected over a time period of 15 s" is a separate clause with its own verb, so the subject of "show" is the singular "the integrated exposure".
Second check: none (judge only)
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Typo Fig. 2 legend, page 2: "The density corresponding to the 12 N-terminal residues of protomers 1 and 4 are shown in the boxed region" — singular subject "The density" with plural verb "are shown" (should be "is shown").
- p. 2 Fig. 2 legend, part A
residues of protomers 1 and 4 are shown in the boxed region
- p. 2 Fig. 2 legend
The density corresponding to the 12 N-terminal residues of protomers 1 and 4 are shown
Judge's note: Read the Fig. 2 legend on the page 2 image; the wording is as quoted. Grammatical agreement error; meaning is unaffected.
Second check: none (judge only)
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Typo Page 4: "this type of gradient in resolution may be informative in its own and could identify regions of the protein" — a word is missing after "own" ("in its own right").
- p. 4 Right column, paragraph beginning "In principle"
its own and could identify regions of the protein
- p. 4 Right column, paragraph beginning 'In principle'
may be informative in
- p. 4 Discussion, right column
may be informative in its own and could identify regions
Judge's note: Read on the page 4 image: the line ends "may be informative in" and the next begins "its own and could identify". Nothing was lost at the line break in extraction; the word is absent in print.
Second check: none (judge only)
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Typo Page 5, two places: "just the first 10 e−/A2 produces density" and "an accumulated dose of ∼45 e−/A2" — the unit should be e−/Å2, as in the same paragraph ("∼3 e−/Å2·s") and on page 4.
- p. 5 Left column, paragraph on beam-induced movement
just the first 10 e−/A2 produces density
- p. 5 Materials and Methods, Data Acquisition
∼45 e−/A2
- p. 4 Left column, for comparison
(10, 20, or 30 e−/Å2)
- p. 5 Materials and Methods, Data Acquisition
accumulated dose of ∼45 e−/A2
Judge's note: The crops show a plain "A" with no ring in both places, while "3-Å resolution" two lines below the first and "∼3 e−/Å2·s" two lines above the second show the ring. Page 4 prints "10, 20, or 30 e−/Å2". Not a text-layer artefact.
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Typo Page 5: "Some protein complexes that are relatively stable in bulk solution may also be more prone to dissociation when it is subject to interfacial forces" — plural "complexes" followed by singular "it is" (should be "they are").
- p. 5 Left column, first paragraph
may also be more prone to dissociation when it is subject to
- p. 5 Discussion
more prone to dissociation when it is subject to
- p. 5 Methods, Image Processing
single-particle cryo-EM specially in the near-atomic
Judge's note: Read on the page 5 image. The only singular noun available, "bulk solution", does not fit the meaning. One reviewer note also raises "specially", which is handled in C014.
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Typo Page 5: "resolution in single-particle cryo-EM specially in the near-atomic resolution regime" — "specially" should be "especially".
- p. 5 Materials and Methods, Image Processing, third paragraph
cryo-EM specially in the near-atomic resolution
- p. 5 Materials and Methods, Image Processing
resolution in single-particle cryo-EM specially in the near-atomic resolution
Judge's note: Read on the page 5 image (Image Processing, third paragraph). The sense is "particularly"; the paper uses "especially" correctly elsewhere (page 1, "especially for proteins such as enzymes").
Second check: none (judge only)