5QYU

PanDDA analysis group deposition -- Auto-refined data of Aar2/RNaseH for ground state model 10

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.51 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.227 

wwPDB Validation   3D Report Full Report


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Literature

F2X-Universal and F2X-Entry: Structurally Diverse Compound Libraries for Crystallographic Fragment Screening.

Wollenhaupt, J., Metz, A., Barthel, T., Lima, G.M.A., Heine, A., Mueller, U., Klebe, G., Weiss, M.S.

(2020) Structure 28: 694-706.e5

  • DOI: 10.1016/j.str.2020.04.019
  • Primary Citation of Related Structures:  
    5QY1, 5QY2, 5QY3, 5QY4, 5QY5, 5QY6, 5QY7, 5QY8, 5QY9, 5QYA, 5QYB, 5QYC, 5QYD, 5QYE, 5QYF, 5QYG, 5QYH, 5QYI, 5QYJ, 5QYK, 5QYL, 5QYM, 5QYN, 5QYO, 5QYP, 5QYQ, 5QYR, 5QYS, 5QYT, 5QYU, 5QYV, 5QYW, 5QYX, 5QYY, 5QYZ, 5QZ0, 5QZ1, 5QZ2, 5QZ3, 5QZ4, 5QZ5, 5QZ6, 5QZ7, 5QZ8, 5QZ9, 5QZA, 5QZB, 5QZC, 5QZD, 5QZE

  • PubMed Abstract: 

    • Crystallographic fragment screening (CFS) provides excellent starting points for projects concerned with drug discovery or biochemical tool compound development. One of the fundamental prerequisites for effective CFS is the availability of a versatile fragment library ...

    Crystallographic fragment screening (CFS) provides excellent starting points for projects concerned with drug discovery or biochemical tool compound development. One of the fundamental prerequisites for effective CFS is the availability of a versatile fragment library. Here, we report on the assembly of the 1,103-compound F2X-Universal Library and its 96-compound sub-selection, the F2X-Entry Screen. Both represent the available fragment chemistry and are highly diverse in terms of their 3D-pharmacophore variations. Validation of the F2X-Entry Screen in CFS campaigns using endothiapepsin and the Aar2/RNaseH complex yielded hit rates of 30% and 21%, respectively, and revealed versatile binding sites. Dry presentation of the libraries allows CFS campaigns to be carried out with or without the co-solvent DMSO present. Most of the hits in our validation campaigns could be reproduced also in the absence of DMSO. Consequently, CFS can be carried out more efficiently and for a wider range of conditions and targets.

    Organizational Affiliation: 

    Helmholtz-Zentrum Berlin, Macromolecular Crystallography, Albert-Einstein-Str. 15, 12489 Berlin, Germany. Electronic address: msweiss@helmholtz-berlin.de.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor 8A258Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP8, DBF3, DNA39, RNA8, SLT21, USA2, YHR165C
UniProt
Find proteins for P33334 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P33334 
Go to UniProtKB:  P33334
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP33334
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
A1 cistron-splicing factor AAR2B308Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: AAR2, YBL074C, YBL06.06, YBL0611
UniProt
Find proteins for P32357 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32357 
Go to UniProtKB:  P32357
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32357
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.51 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.227 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.748α = 90
b = 81.382β = 108.78
c = 92.808γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing
PHENIXrefinement

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-06-10
    Type: Initial release