6Y2N

Crystal structure of ribonucleotide reductase R2 subunit solved by serial synchrotron crystallography


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.176 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Current status and future opportunities for serial crystallography at MAX IV Laboratory.

Shilova, A.Lebrette, H.Aurelius, O.Nan, J.Welin, M.Kovacic, R.Ghosh, S.Safari, C.Friel, R.J.Milas, M.Matej, Z.Hogbom, M.Branden, G.Kloos, M.Shoeman, R.L.Doak, B.Ursby, T.Hakansson, M.Logan, D.T.Mueller, U.

(2020) J Synchrotron Radiat 27: 1095-1102

  • DOI: https://doi.org/10.1107/S1600577520008735
  • Primary Citation of Related Structures:  
    6Y2N, 6Y4C, 6Y78

  • PubMed Abstract: 

    Over the last decade, serial crystallography, a method to collect complete diffraction datasets from a large number of microcrystals delivered and exposed to an X-ray beam in random orientations at room temperature, has been successfully implemented at X-ray free-electron lasers and synchrotron radiation facility beamlines. This development relies on a growing variety of sample presentation methods, including different fixed target supports, injection methods using gas-dynamic virtual-nozzle injectors and high-viscosity extrusion injectors, and acoustic levitation of droplets, each with unique requirements. In comparison with X-ray free-electron lasers, increased beam time availability makes synchrotron facilities very attractive to perform serial synchrotron X-ray crystallography (SSX) experiments. Within this work, the possibilities to perform SSX at BioMAX, the first macromolecular crystallography beamline at  MAX IV Laboratory in Lund, Sweden, are described, together with case studies from the SSX user program: an implementation of a high-viscosity extrusion injector to perform room temperature serial crystallography at BioMAX using two solid supports - silicon nitride membranes (Silson, UK) and XtalTool (Jena Bioscience, Germany). Future perspectives for the dedicated serial crystallography beamline MicroMAX at MAX IV Laboratory, which will provide parallel and intense micrometre-sized X-ray beams, are discussed.


  • Organizational Affiliation

    MAX IV Laboratory, Lund University, Fotongatan 2, Lund 22484, Sweden.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ribonucleoside-diphosphate reductase subunit beta341Saccharopolyspora erythraea NRRL 2338Mutation(s): 0 
Gene Names: nrdBSACE_1282A8924_1677
EC: 1.17.4.1
UniProt
Find proteins for A4F980 (Saccharopolyspora erythraea (strain ATCC 11635 / DSM 40517 / JCM 4748 / NBRC 13426 / NCIMB 8594 / NRRL 2338))
Explore A4F980 
Go to UniProtKB:  A4F980
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA4F980
Sequence Annotations
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.176 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.32α = 90
b = 64.32β = 90
c = 153.15γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MxCuBEdata collection
PHENIXphasing
CrystFELdata scaling
Cootmodel building
CrystFELdata reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Research CouncilSweden2017-04018
Knut and Alice Wallenberg FoundationSwedenWallenberg Academy Fellows 2017.0275
European Research Council (ERC)SwedenHIGH-GEAR 724394

Revision History  (Full details and data files)

  • Version 1.0: 2020-10-07
    Type: Initial release
  • Version 1.1: 2024-05-01
    Changes: Data collection, Database references, Refinement description