Femtosecond X-Ray Protein Nanocrystallography
2011 · paper · Instrumentation
Concerns femtosecond X-ray nanocrystallography of proteins. The text provided contains only author and affiliation details, so it does not show what the study found.
1 finding
Wording Fig. 4 caption: "The decrease in irradiance for 200-fs pulses and d < 25 Å indicates radiation damage" uses "irradiance" for the plotted quantity, which the same caption calls "integrated Bragg intensities", the y-axis labels "Intensity (photons)" and the main text calls "scattering strength"; elsewhere the paper defines irradiance as the incident pulse power density ("irradiance (or power density) of focused pulses", "peak power density (irradiance) in excess of 10^16 W cm−2").
- p. 13 Figure 4 caption
The decrease in irradiance for 200-fs pulses and d < 25 Å
- p. 13 Figure 4, y-axis label
Intensity (photons)
- p. 3 Main text, first paragraph
the irradiance (or power density) of focused pulses
- p. 13 Figure 4 caption
The decrease in
Judge's note: Viewed the full page 13 image and the caption crop: the y-axis reads "Intensity (photons)" and the caption's last sentence reads "The decrease in irradiance for 200-fs pulses and d < 25 Å". Searched the text for "irradiance": the other four uses (PDF p3, the 10^5-fold "pulse irradiance" sentence, and two in Methods) all mean the incident beam's power density in W cm−2, and the results text describes the Fig. 4 effect as "a decrease in scattering strength at resolutions beyond 25 Å". So the caption uses a term the paper reserves for a different quantity. The meaning is recoverable (loosely, diffracted irradiance at the detector) and no number or conclusion is affected, hence a wording inconsistency rated S3 and bucketed as an observation. The 25 Å threshold agrees between caption and text.
Second check: another model agreed
Report a problem with this finding
6 minor (typos and the like; most checked by the judge only)
Wording Hit threshold is "with ten or more spots" in the main text but "(more than ten detected peaks)" in Methods.
- p. 4 Main text, Monte Carlo integration paragraph
with ten or more spots could be consistently indexed
- p. 6 Methods, 3D merging of intensities
(more than ten detected peaks)
- p. 4 Results, Monte Carlo integration paragraph
with ten or more spots
Judge's note: Pages 4 and 6 images. The 'over 13%' in the main text matches 15,445/112,725 from the Methods hit population, so both phrases describe the same set with thresholds that differ by one peak (>=10 versus >10). Negligible practical effect.
Second check: another model agreed
Report a problem with this finding
Typo "(1-MD a molecular mass, 36 proteins, 381 cofactors)": the unit MDa is split by a space; should read "1-MDa molecular mass".
- p. 3 Main text, second paragraph
(1-MD a molecular mass, 36 proteins, 381 cofactors)
- p. 3 Introduction, 2nd paragraph
(1-MD a
- p. 3 Paragraph 2, photosystem I description
(1-MD a molecular mass
Judge's note: Page 3 image shows '(1-MD a' at the end of a line with a visible space between 'MD' and 'a', then 'molecular mass' on the next line. Present in the typeset PDF, not only in the text layer.
Second check: none (judge only)
Report a problem with this finding
Typo Reference 6: "femtosecond X-raypulses" should read "femtosecond X-ray pulses".
- p. 8 Reference 6
femtosecond X-raypulses
- p. 8 Reference 6
Neutze R, Wout R
Judge's note: Page 8 image shows 'X-raypulses' with no space. The author-name point raised alongside it is handled in C012.
Second check: none (judge only)
Report a problem with this finding
Typo Reference 6: second author printed as "Neutze R, Wout R, van der Spoel D"; the surname is believed to be Wouts.
- p. 8 Reference 6
Neutze R, Wout R, van der Spoel D
Only the authors can say what is right here.
Judge's note: Rests on outside knowledge: that the second author of Neutze et al., Nature 406:752 (2000) is R. Wouts. The page 8 image prints 'Wout R' as quoted; the correct spelling cannot be checked from the files.
Second check: none (judge only)
Report a problem with this finding
Typo Reference 34 title is misspelt: "Refinement of macromolecular structures by the maximum-likehood method"; it should read "maximum-likelihood".
- p. 9 Reference 34
maximum-likehood method
- p. 9
maximum-likehood method. Acta Crystallogr D. 1997
Judge's note: The crop of PDF page 9 (reference list) shows reference 34 printed as "maximum-likehood method. Acta Crystallogr D. 1997; 53:240–255." The text layer (main.txt line 462) matches the image. The word sits in the middle of a line, so this is not a hyphenation or line-break artefact. "likehood" is not a word, and the obvious fix is "likelihood". This is a cosmetic misspelling in a reference title.
Second check: none (judge only)
Report a problem with this finding
Typo Figure 3a panel labels read "Upper font detector" and "Lower font detector"; should be "front detector" (caption: "recorded on the front pnCCDs").
- p. 12 Figure 3a, label inside upper sub-panel
Upper font detector
- p. 12 Figure 3a, label inside lower sub-panel
Lower font detector
- p. 12 Figure 3 caption
Diffraction pattern recorded on the front pnCCDs
- p. 12 Figure 3a, panel labels
Upper font detector / Lower font detector
Judge's note: Page 12 image: both labels inside panel a read 'font detector'. The caption and the text call these the front pnCCDs / front detector throughout. The labels are in the figure artwork, not the text layer.
Second check: none (judge only)