5L9J

Room temperature X-ray diffraction of tetragonal HEWL. First data set (0.31 MGy)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.111 

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: 10.1107/S1600577516018452
  • Primary Citation of Related Structures:  

  • 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 pro ...

    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 D1/2 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysozyme C
A
129Gallus gallusMutation(s): 0 
Gene Names: LYZ
EC: 3.2.1.17
Find proteins for P00698 (Gallus gallus)
Go to Gene View: LYZ
Go to UniProtKB:  P00698
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.111 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 79.244α = 90.00
b = 79.244β = 90.00
c = 37.896γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Consejo de Seguridad NuclearSpain--

Revision History 

  • Version 1.0: 2016-06-22
    Type: Initial release
  • Version 1.1: 2016-12-14
    Type: Database references
  • Version 1.2: 2017-01-11
    Type: Database references