5LA5

Room temperature X-ray diffraction of tetragonal HEWL. Second data set (0.62 MGy)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.143 
  • R-Value Observed: 0.146 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Uridine as a new scavenger for synchrotron-based structural biology techniques.

Crosas, E.Castellvi, A.Crespo, I.Fulla, D.Gil-Ortiz, F.Fuertes, G.Kamma-Lorger, C.S.Malfois, M.Aranda, M.A.Juanhuix, J.

(2017) J Synchrotron Radiat 24: 53-62

  • DOI: https://doi.org/10.1107/S1600577516018452
  • Primary Citation of Related Structures:  
    5L9J, 5LA5, 5LA8, 5LAF, 5LAG, 5LAN

  • PubMed Abstract: 

    Macromolecular crystallography (MX) and small-angle X-ray scattering (SAXS) studies on proteins at synchrotron light sources are commonly limited by the structural damage produced by the intense X-ray beam. Several effects, such as aggregation in protein solutions and global and site-specific damage in crystals, reduce the data quality or even introduce artefacts that can result in a biologically misguiding structure. One strategy to reduce these negative effects is the inclusion of an additive in the buffer solution to act as a free radical scavenger. Here the properties of uridine as a scavenger for both SAXS and MX experiments on lysozyme at room temperature are examined. In MX experiments, upon addition of uridine at 1 M, the critical dose D 1/2 is increased by a factor of ∼1.7, a value similar to that obtained in the presence of the most commonly used scavengers such as ascorbate and sodium nitrate. Other figures of merit to assess radiation damage show a similar trend. In SAXS experiments, the scavenging effect of 40 mM uridine is similar to that of 5% v/v glycerol, and greater than 2 mM DTT and 1 mM ascorbic acid. In all cases, the protective effect of uridine is proportional to its concentration.


  • Organizational Affiliation

    ALBA Synchrotron, Carrer de la llum 2-26, 08290 Cerdanyola del Vallès, Barcelona, Spain.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lysozyme C129Gallus gallusMutation(s): 0 
EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus)
Explore P00698 
Go to UniProtKB:  P00698
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00698
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.143 
  • R-Value Observed: 0.146 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.285α = 90
b = 79.285β = 90
c = 37.88γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Spanish Nuclear Safety CouncilSpain--

Revision History  (Full details and data files)

  • Version 1.0: 2016-12-21
    Type: Initial release
  • Version 1.1: 2017-01-11
    Changes: Database references
  • Version 1.2: 2024-01-10
    Changes: Data collection, Database references, Refinement description