5JOM

X-ray structure of CO-bound sperm whale myoglobin using a fixed target crystallography chip


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Fixed target combined with spectral mapping: approaching 100% hit rates for serial crystallography.

Oghbaey, S.Sarracini, A.Ginn, H.M.Pare-Labrosse, O.Kuo, A.Marx, A.Epp, S.W.Sherrell, D.A.Eger, B.T.Zhong, Y.Loch, R.Mariani, V.Alonso-Mori, R.Nelson, S.Lemke, H.T.Owen, R.L.Pearson, A.R.Stuart, D.I.Ernst, O.P.Mueller-Werkmeister, H.M.Miller, R.J.

(2016) Acta Crystallogr D Struct Biol 72: 944-955

  • DOI: 10.1107/S2059798316010834

  • PubMed Abstract: 
  • The advent of ultrafast highly brilliant coherent X-ray free-electron laser sources has driven the development of novel structure-determination approaches for proteins, and promises visualization of protein dynamics on sub-picosecond timescales with ...

    The advent of ultrafast highly brilliant coherent X-ray free-electron laser sources has driven the development of novel structure-determination approaches for proteins, and promises visualization of protein dynamics on sub-picosecond timescales with full atomic resolution. Significant efforts are being applied to the development of sample-delivery systems that allow these unique sources to be most efficiently exploited for high-throughput serial femtosecond crystallography. Here, the next iteration of a fixed-target crystallography chip designed for rapid and reliable delivery of up to 11 259 protein crystals with high spatial precision is presented. An experimental scheme for predetermining the positions of crystals in the chip by means of in situ spectroscopy using a fiducial system for rapid, precise alignment and registration of the crystal positions is presented. This delivers unprecedented performance in serial crystallography experiments at room temperature under atmospheric pressure, giving a raw hit rate approaching 100% with an effective indexing rate of approximately 50%, increasing the efficiency of beam usage and allowing the method to be applied to systems where the number of crystals is limited.


    Organizational Affiliation

    Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada.,Atomically Resolved Dynamics, Max-Planck-Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, Hamburg, Germany.,Hamburg Centre for Ultrafast Imaging, University of Hamburg, Hamburg, Germany.,Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 ODE, England.,Center for Free-Electron Laser Science, DESY, 22607 Hamburg, Germany.,Department of Physics and Chemistry, University of Toronto, 60 St George Street, Toronto, ON M5S 1A7, Canada.,SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA.,Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, England.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Myoglobin
A
154Physeter macrocephalusMutation(s): 0 
Gene Names: MB
Find proteins for P02185 (Physeter macrocephalus)
Go to Gene View: MB
Go to UniProtKB:  P02185
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
HEM
Query on HEM

Download SDF File 
Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
CMO
Query on CMO

Download SDF File 
Download CCD File 
A
CARBON MONOXIDE
C O
UGFAIRIUMAVXCW-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.212 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 38.130α = 90.00
b = 46.483β = 90.00
c = 84.521γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
DIALSdata scaling
PHASERphasing
CPPXFELdata reduction
CPPXFELdata processing
CPPXFELdata scaling
Cheetahdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Natural Sciences and Engineering Research Council (Canada)Canada--
Max Planck SocietyGermany--
Canadian Institute for Advanced ResearchCanada--
Canada Excellence Research Chair ProgramCanada--
Anne and Max Tanenbaum Chair in Neuroscience at the University of TorontoCanada--
People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013)GermanyREA grant agreement no. 623994
Department of Energy (United States)United StatesContract No. DE-AC02-76SF00515

Revision History 

  • Version 1.0: 2016-08-17
    Type: Initial release
  • Version 1.1: 2017-09-13
    Type: Author supporting evidence, Derived calculations
  • Version 1.2: 2017-11-22
    Type: Refinement description
  • Version 1.3: 2018-02-14
    Type: Data collection
  • Version 1.4: 2018-04-18
    Type: Data collection