Evidence map›Paper›PMID 34783106›Full record

ArticleProtein science : a publication of the Protein Society2022

Optimal structure determination from sub-optimal diffraction data.

Wladek Minor, Marcin Cymborowski, Dominika Borek, David R Cooper, Maksymilian Chruszcz, Zbyszek Otwinowski

Abstract read
In one paragraph

Article in Protein science : a publication of the Protein Society, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.

0numbers the graph read from it
0cells of the map it votes in
7citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

7 citing papers in PubMed.

  1. Article
  2. Article
  3. Long Dynamic β1-β2 Loops inInternational journal of molecular sciences · 2024
    Article
  4. Article
  5. Structural Basis of Nucleic Acid Recognition and 6mA Demethylation byInternational journal of molecular sciences · 2024
    Article
  6. Article
  7. Optimal structure determination from sub-optimal diffraction data.Protein science : a publication of the Protein Society · 2022
    Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

6 authors.

Wladek MinorDepartment of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia.ORCID 0000-0001-7075-7090
Marcin CymborowskiDepartment of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia.ORCID 0000-0001-6511-7945
Dominika BorekDepartment of Biophysics, The University of Texas Southwestern Medical Center, Dallas, Texas.ORCID 0000-0002-4321-6253
David R CooperDepartment of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia.ORCID 0000-0001-5240-9789
Maksymilian ChruszczDepartment of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina.ORCID 0000-0001-7521-5485
Zbyszek OtwinowskiDepartment of Biophysics, The University of Texas Southwestern Medical Center, Dallas, Texas.ORCID 0000-0003-3640-8545

Funding

X-RAY CRYSTALLOGRAPHY OF MACROMOLECULESR01GM053163 · NIGMS · UT SOUTHWESTERN MEDICAL CENTER · PI MINOR, WLADEK, OTWINOWSKI, ZBYSZEK · 1996 to 2014
$6.3M
From complex data to complex structures: new methods for structural biologyR35GM145365 · NIGMS · UT SOUTHWESTERN MEDICAL CENTER · PI ZBYSZEK OTWINOWSKI · 2022 to 2026
$2.3M
Reproducible, Unbiased Ligand Identification Assisted by Artificial Intelligence and Development of Ligand Reference LibrariesR01GM132595 · NIGMS · UNIVERSITY OF VIRGINIA · PI MINOR, WLADEK · 2019 to 2022
$2.3M
X-ray data analysis in the presence of structural variability - Administrative SupplementR01GM117080 · NIGMS · UT SOUTHWESTERN MEDICAL CENTER · PI MINOR, WLADEK, OTWINOWSKI, ZBYSZEK · 2015 to 2018
$1.4M
Accurate measurements of phasing signal to determine macromolecular structuresR01GM118619 · NIGMS · UT SOUTHWESTERN MEDICAL CENTER · PI OTWINOWSKI, ZBYSZEK · 2017 to 2020
$1.3M
Radioprotectants for structural biologyR21GM126406 · NIGMS · UT SOUTHWESTERN MEDICAL CENTER · PI BOREK, DOMINIKA MARTA · 2018 to 2019
$446k
NIGMS NIH HHS R01 GM053163NIGMS NIH HHS R01 GM117080NIGMS NIH HHS R01 GM118619NIGMS NIH HHS R01 GM132595NIGMS NIH HHS R21 GM126406NIGMS NIH HHS R35 GM145365
6 · The paper itself

Abstract

Herein we present the newest version of the HKL-3000 system that integrates data collection, data reduction, phasing, model building, refinement, and validation. The system significantly accelerates the process of structure determination and has proven its high value for the determination of very high-quality structures. The heuristic for choosing the best approach for every step of structure determination for various quality samples and diffraction data has been optimized. The latest modifications increase the likelihood of a successful structure determination with challenging data. The HKL-3000 is a successor of HKL and HKL-2000 programs. The use of the HKL family of programs has been reported for over 73,000 PDB deposits, that is, almost 50% of macromolecular structures determined with X-ray diffraction.

Indexed as

Models, MolecularSoftwareX-Ray DiffractionMolecular Structurehigh-quality macromolecular structuresmacromolecular structure determinationoptimal structure determination

Identifiers

PMID34783106
PMCPMC8740829

What OpenQuestion holds

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.