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Tytuł:
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Measurement of atom resolvability in cryo-EM maps with Q-scores.
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Autorzy:
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Pintilie G; Department of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA, USA. .
Zhang K; Department of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA, USA.
Su Z; Department of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA, USA.
Li S; Department of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA, USA.
Schmid MF; Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA, USA.
Chiu W; Department of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA, USA. .; Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA, USA. .
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Źródło:
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Nature methods [Nat Methods] 2020 Mar; Vol. 17 (3), pp. 328-334. Date of Electronic Publication: 2020 Feb 10.
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Typ publikacji:
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Journal Article; Research Support, N.I.H., Extramural
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Język:
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English
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Imprint Name(s):
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Original Publication: New York, NY : Nature Pub. Group, c2004-
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MeSH Terms:
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Cryoelectron Microscopy*
Apoferritins/*chemistry
Algorithms ; Animals ; Fourier Analysis ; Humans ; Hydrogen Bonding ; Ligands ; Macromolecular Substances/chemistry ; Mice ; Microscopy, Electron ; Models, Molecular ; Normal Distribution ; Protein Structure, Secondary ; RNA/chemistry ; Solvents/chemistry
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References:
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Grant Information:
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P41 GM103311 United States GM NIGMS NIH HHS; P41 GM103832 United States GM NIGMS NIH HHS; R01 GM079429 United States GM NIGMS NIH HHS; S10 OD021600 United States OD NIH HHS
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Substance Nomenclature:
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0 (Ligands)
0 (Macromolecular Substances)
0 (Solvents)
63231-63-0 (RNA)
9013-31-4 (Apoferritins)
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Entry Date(s):
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Date Created: 20200212 Date Completed: 20200417 Latest Revision: 20240330
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Update Code:
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20240330
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PubMed Central ID:
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PMC7446556
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DOI:
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10.1038/s41592-020-0731-1
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PMID:
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32042190
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Cryogenic electron microscopy (cryo-EM) maps are now at the point where resolvability of individual atoms can be achieved. However, resolvability is not necessarily uniform throughout the map. We introduce a quantitative parameter to characterize the resolvability of individual atoms in cryo-EM maps, the map Q-score. Q-scores can be calculated for atoms in proteins, nucleic acids, water, ligands and other solvent atoms, using models fitted to or derived from cryo-EM maps. Q-scores can also be averaged to represent larger features such as entire residues and nucleotides. Averaged over entire models, Q-scores correlate very well with the estimated resolution of cryo-EM maps for both protein and RNA. Assuming the models they are calculated from are well fitted to the map, Q-scores can be used as a measure of resolvability in cryo-EM maps at various scales, from entire macromolecules down to individual atoms. Q-score analysis of multiple cryo-EM maps of the same proteins derived from different laboratories confirms the reproducibility of structural features from side chains down to water and ion atoms.