8PX0

Structure of ribonuclease A, solved at wavelength 2.75 A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 

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Ligand Structure Quality Assessment 


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Literature

Experimental phasing opportunities for macromolecular crystallography at very long wavelengths.

El Omari, K.Duman, R.Mykhaylyk, V.Orr, C.M.Latimer-Smith, M.Winter, G.Grama, V.Qu, F.Bountra, K.Kwong, H.S.Romano, M.Reis, R.I.Vogeley, L.Vecchia, L.Owen, C.D.Wittmann, S.Renner, M.Senda, M.Matsugaki, N.Kawano, Y.Bowden, T.A.Moraes, I.Grimes, J.M.Mancini, E.J.Walsh, M.A.Guzzo, C.R.Owens, R.J.Jones, E.Y.Brown, D.G.Stuart, D.I.Beis, K.Wagner, A.

(2023) Commun Chem 6: 219-219

  • DOI: https://doi.org/10.1038/s42004-023-01014-0
  • Primary Citation of Related Structures:  
    8PWN, 8PX0, 8PX1, 8PX4, 8PX5, 8PX7, 8PX9, 8PXC, 8PXG, 8PXH, 8PXJ, 8PXK, 8PXL, 8PYV, 8PYZ, 8PZ4, 8PZ5

  • PubMed Abstract: 

    Despite recent advances in cryo-electron microscopy and artificial intelligence-based model predictions, a significant fraction of structure determinations by macromolecular crystallography still requires experimental phasing, usually by means of single-wavelength anomalous diffraction (SAD) techniques. Most synchrotron beamlines provide highly brilliant beams of X-rays of between 0.7 and 2 Å wavelength. Use of longer wavelengths to access the absorption edges of biologically important lighter atoms such as calcium, potassium, chlorine, sulfur and phosphorus for native-SAD phasing is attractive but technically highly challenging. The long-wavelength beamline I23 at Diamond Light Source overcomes these limitations and extends the accessible wavelength range to λ = 5.9 Å. Here we report 22 macromolecular structures solved in this extended wavelength range, using anomalous scattering from a range of elements which demonstrate the routine feasibility of lighter atom phasing. We suggest that, in light of its advantages, long-wavelength crystallography is a compelling option for experimental phasing.


  • Organizational Affiliation

    Diamond Light Source, Harwell Science and Innovation Campus, -, OX110DE, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ribonuclease pancreatic
A, B
124Bos taurusMutation(s): 0 
Gene Names: RNASE1RNS1
EC: 4.6.1.18
UniProt
Find proteins for P61823 (Bos taurus)
Explore P61823 
Go to UniProtKB:  P61823
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61823
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
0U
Query on 0U

Download Ideal Coordinates CCD File 
C [auth A]L-URIDINE-5'-MONOPHOSPHATE
C9 H13 N2 O9 P
DJJCXFVJDGTHFX-PSQAKQOGSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.98α = 90
b = 32.62β = 90.16
c = 72.49γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
HKL2Mapphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Diamond Light SourceUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2023-10-25
    Type: Initial release