6N00

Fluoroacetate dehalogenase, room temperature structure, using last 1 degree of total 3 degree oscillation and 144 kGy dose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Fixed-target serial oscillation crystallography at room temperature.

Wierman, J.L.Pare-Labrosse, O.Sarracini, A.Besaw, J.E.Cook, M.J.Oghbaey, S.Daoud, H.Mehrabi, P.Kriksunov, I.Kuo, A.Schuller, D.J.Smith, S.Ernst, O.P.Szebenyi, D.M.E.Gruner, S.M.Miller, R.J.D.Finke, A.D.

(2019) IUCrJ 6: 305-316

  • DOI: https://doi.org/10.1107/S2052252519001453
  • Primary Citation of Related Structures:  
    6MUH, 6MUY, 6MUZ, 6MV0, 6MZZ, 6N00, 6N02, 6N03

  • PubMed Abstract: 

    A fixed-target approach to high-throughput room-temperature serial synchrotron crystallography with oscillation is described. Patterned silicon chips with microwells provide high crystal-loading density with an extremely high hit rate. The microfocus, undulator-fed beamline at CHESS, which has compound refractive optics and a fast-framing detector, was built and optimized for this experiment. The high-throughput oscillation method described here collects 1-5° of data per crystal at room temperature with fast (10° s -1 ) oscillation rates and translation times, giving a crystal-data collection rate of 2.5 Hz. Partial datasets collected by the oscillation method at a storage-ring source provide more complete data per crystal than still images, dramatically lowering the total number of crystals needed for a complete dataset suitable for structure solution and refinement - up to two orders of magnitude fewer being required. Thus, this method is particularly well suited to instances where crystal quantities are low. It is demonstrated, through comparison of first and last oscillation images of two systems, that dose and the effects of radiation damage can be minimized through fast rotation and low angular sweeps for each crystal.


  • Organizational Affiliation

    MacCHESS, Cornell University, Ithaca, NY 14853, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fluoroacetate dehalogenase
A, B
306Rhodopseudomonas palustris CGA009Mutation(s): 0 
Gene Names: RPA1163
EC: 3.8.1.3
UniProt
Find proteins for Q6NAM1 (Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009))
Explore Q6NAM1 
Go to UniProtKB:  Q6NAM1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6NAM1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download Ideal Coordinates CCD File 
C [auth B]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.6α = 90
b = 79.1β = 103
c = 83.8γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM-103485
National Science Foundation (NSF, United States)United StatesDMR-1332208

Revision History  (Full details and data files)

  • Version 1.0: 2019-03-27
    Type: Initial release
  • Version 1.1: 2019-11-27
    Changes: Author supporting evidence
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description