6QQH

Cryogenic temperature structure of the ground state of AtPhot2LOV2 recorded after an accumulated dose of 2.68 MGy


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.38 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.140 
  • R-Value Observed: 0.141 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Specific radiation damage is a lesser concern at room temperature.

Gotthard, G.Aumonier, S.De Sanctis, D.Leonard, G.von Stetten, D.Royant, A.

(2019) IUCrJ 6: 665-680

  • DOI: https://doi.org/10.1107/S205225251900616X
  • Primary Citation of Related Structures:  
    6QQ8, 6QQ9, 6QQA, 6QQB, 6QQC, 6QQD, 6QQE, 6QQF, 6QQH, 6QQI, 6QQJ, 6QQK, 6QSA

  • PubMed Abstract: 

    Carrying out macromolecular crystallography (MX) experiments at cryogenic temperatures significantly slows the rate of global radiation damage, thus facilitating the solution of high-resolution crystal structures of macromolecules. However, cryo-MX experiments suffer from the early onset of so-called specific radiation damage that affects certain amino-acid residues and, in particular, the active sites of many proteins. Here, a series of MX experiments are described which suggest that specific and global radiation damage are much less decoupled at room temperature than they are at cryogenic temperatures. The results reported here demonstrate the interest in reviving the practice of collecting MX diffraction data at room temperature and allow structural biologists to favourably envisage the development of time-resolved MX experiments at synchrotron sources.


  • Organizational Affiliation

    European Synchrotron Radiation Facility, F-38043 Grenoble, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phototropin-2128Arabidopsis thalianaMutation(s): 0 
Gene Names: PHOT2CAV1KIN7NPL1At5g58140K21L19.6
EC: 2.7.11.1
UniProt
Find proteins for P93025 (Arabidopsis thaliana)
Explore P93025 
Go to UniProtKB:  P93025
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP93025
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FMN
Query on FMN

Download Ideal Coordinates CCD File 
B [auth A]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.38 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.140 
  • R-Value Observed: 0.141 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.148α = 90
b = 40.148β = 90
c = 131.575γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-19
    Type: Initial release
  • Version 1.1: 2019-07-31
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description