2A7G

On the Routine Use of Soft X-Rays in Macromolecular Crystallography, Part III- The Optimal Data Collection Wavelength


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.162 

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This is version 1.3 of the entry. See complete history


Literature

On the routine use of soft X-rays in macromolecular crystallography. Part III. The optimal data-collection wavelength.

Mueller-Dieckmann, C.Panjikar, S.Tucker, P.A.Weiss, M.S.

(2005) Acta Crystallogr D Biol Crystallogr 61: 1263-1272

  • DOI: https://doi.org/10.1107/S0907444905021475
  • Primary Citation of Related Structures:  
    2A7A, 2A7B, 2A7C, 2A7D, 2A7E, 2A7F, 2A7G, 2A7H, 2A7I, 2A7J

  • PubMed Abstract: 

    Complete and highly redundant data sets were collected at different wavelengths between 0.80 and 2.65 A for a total of ten different protein and DNA model systems. The magnitude of the anomalous signal-to-noise ratio as assessed by the quotient R(anom)/R(r.i.m.) was found to be influenced by the data-collection wavelength and the nature of the anomalously scattering substructure. By utilizing simple empirical correlations, for instance between the estimated deltaF/F and the expected R(anom) or the data-collection wavelength and the expected R(r.i.m.), the wavelength at which the highest anomalous signal-to-noise ratio can be expected could be estimated even before the experiment. Almost independent of the nature of the anomalously scattering substructure and provided that no elemental X-ray absorption edge is nearby, this optimal wavelength is 2.1 A.


  • Organizational Affiliation

    EMBL Hamburg Outstation, c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
thermolysinA [auth E]316Bacillus thermoproteolyticusMutation(s): 0 
EC: 2.2.1.2 (PDB Primary Data), 3.4.24.27 (UniProt)
UniProt
Find proteins for P00800 (Bacillus thermoproteolyticus)
Explore P00800 
Go to UniProtKB:  P00800
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00800
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DMS
Query on DMS

Download Ideal Coordinates CCD File 
I [auth E],
J [auth E]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ZN
Query on ZN

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B [auth E]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACY
Query on ACY

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K [auth E]ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
C [auth E]
D [auth E]
E
F [auth E]
G [auth E]
C [auth E],
D [auth E],
E,
F [auth E],
G [auth E],
H [auth E]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.162 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.99α = 90
b = 92.99β = 90
c = 130.21γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-07-19
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Derived calculations