7AI8 | pdb_00007ai8

Structure of Ribonucleotide reductase R2 from Escherichia coli collected by still serial crystallography on a COC membrane at a synchrotron source


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.219 (Depositor), 0.222 (DCC) 
  • R-Value Work: 
    0.190 (Depositor), 0.192 (DCC) 
  • R-Value Observed: 
    0.191 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7AI8

This is version 1.2 of the entry. See complete history

Literature

Versatile microporous polymer-based supports for serial macromolecular crystallography.

Martiel, I.Beale, J.H.Karpik, A.Huang, C.Y.Vera, L.Olieric, N.Wranik, M.Tsai, C.J.Muhle, J.Aurelius, O.John, J.Hogbom, M.Wang, M.Marsh, M.Padeste, C.

(2021) Acta Crystallogr D Struct Biol 77: 1153-1167

  • DOI: https://doi.org/10.1107/S2059798321007324
  • Primary Citation Related Structures: 
    7AC2, 7AC3, 7AC4, 7AC5, 7AC6, 7AI8, 7AI9

  • PubMed Abstract: 

    Serial data collection has emerged as a major tool for data collection at state-of-the-art light sources, such as microfocus beamlines at synchrotrons and X-ray free-electron lasers. Challenging targets, characterized by small crystal sizes, weak diffraction and stringent dose limits, benefit most from these methods. Here, the use of a thin support made of a polymer-based membrane for performing serial data collection or screening experiments is demonstrated. It is shown that these supports are suitable for a wide range of protein crystals suspended in liquids. The supports have also proved to be applicable to challenging cases such as membrane proteins growing in the sponge phase. The sample-deposition method is simple and robust, as well as flexible and adaptable to a variety of cases. It results in an optimally thin specimen providing low background while maintaining minute amounts of mother liquor around the crystals. The 2 × 2 mm area enables the deposition of up to several microlitres of liquid. Imaging and visualization of the crystals are straightforward on the highly transparent membrane. Thanks to their affordable fabrication, these supports have the potential to become an attractive option for serial experiments at synchrotrons and free-electron lasers.


  • Organizational Affiliation
    • Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland.

Macromolecule Content 

  • Total Structure Weight: 43.67 kDa 
  • Atom Count: 2,897 
  • Modeled Residue Count: 339 
  • Deposited Residue Count: 376 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Ribonucleoside-diphosphate reductase 1 subunit beta376Escherichia coli K-12Mutation(s): 0 
Gene Names: nrdBftsBb2235JW2229
EC: 1.17.4.1
UniProt
Find proteins for P69924 (Escherichia coli (strain K12))
Explore P69924 
Go to UniProtKB:  P69924
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP69924
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.219 (Depositor), 0.222 (DCC) 
  • R-Value Work:  0.190 (Depositor), 0.192 (DCC) 
  • R-Value Observed: 0.191 (Depositor) 
Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.35α = 90
b = 90.35β = 90
c = 208.55γ = 120
Software Package:
Software NamePurpose
CrystFELdata reduction
CrystFELdata scaling
PHENIXrefinement
PHENIXphasing
Cootmodel building

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Knut and Alice Wallenberg FoundationSweden--
European Research Council (ERC)European UnionHIGH-GEAR 724394

Revision History  (Full details and data files)

  • Version 1.0: 2021-09-01
    Type: Initial release
  • Version 1.1: 2021-09-29
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description