Thermolysin structure determined by free-electron laser

Experimental Data Snapshot

  • Resolution: 2.10 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.220 

wwPDB Validation   3D Report Full Report

This is version 1.6 of the entry. See complete history


Accurate macromolecular structures using minimal measurements from X-ray free-electron lasers.

Hattne, J.Echols, N.Tran, R.Kern, J.Gildea, R.J.Brewster, A.S.Alonso-Mori, R.Glockner, C.Hellmich, J.Laksmono, H.Sierra, R.G.Lassalle-Kaiser, B.Lampe, A.Han, G.Gul, S.DiFiore, D.Milathianaki, D.Fry, A.R.Miahnahri, A.White, W.E.Schafer, D.W.Seibert, M.M.Koglin, J.E.Sokaras, D.Weng, T.C.Sellberg, J.Latimer, M.J.Glatzel, P.Zwart, P.H.Grosse-Kunstleve, R.W.Bogan, M.J.Messerschmidt, M.Williams, G.J.Boutet, S.Messinger, J.Zouni, A.Yano, J.Bergmann, U.Yachandra, V.K.Adams, P.D.Sauter, N.K.

(2014) Nat Methods 11: 545-548

  • DOI: https://doi.org/10.1038/nmeth.2887
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    X-ray free-electron laser (XFEL) sources enable the use of crystallography to solve three-dimensional macromolecular structures under native conditions and without radiation damage. Results to date, however, have been limited by the challenge of deriving accurate Bragg intensities from a heterogeneous population of microcrystals, while at the same time modeling the X-ray spectrum and detector geometry. Here we present a computational approach designed to extract meaningful high-resolution signals from fewer diffraction measurements.

  • Organizational Affiliation

    Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Thermolysin316Bacillus thermoproteolyticusMutation(s): 0 
Find proteins for P00800 (Bacillus thermoproteolyticus)
Explore P00800 
Go to UniProtKB:  P00800
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00800
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.8933α = 90
b = 92.8933β = 90
c = 130.438γ = 120
Software Package:
Software NamePurpose

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM095887
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM102520
Department of Energy (DOE, United States)United StatesDE-AC02-05CH11231
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM055302
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP41GM103393

Revision History  (Full details and data files)

  • Version 1.0: 2014-03-12
    Type: Initial release
  • Version 1.1: 2014-06-18
    Changes: Database references
  • Version 1.2: 2015-02-04
    Changes: Derived calculations
  • Version 1.3: 2017-09-27
    Changes: Advisory, Author supporting evidence, Database references, Derived calculations, Other, Source and taxonomy, Structure summary
  • Version 1.4: 2019-12-04
    Changes: Author supporting evidence
  • Version 1.5: 2023-08-16
    Changes: Data collection, Database references, Refinement description
  • Version 1.6: 2023-09-27
    Changes: Refinement description