4PNJ

Recombinant Sperm Whale P6 Myoglobin Solved with Single Pulse Free Electron Laser Data


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.36 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.159 

wwPDB Validation 3D Report Full Report


This is version 1.6 of the entry. See complete history

Literature

Goniometer-based femtosecond crystallography with X-ray free electron lasers.

Cohen, A.E.Soltis, S.M.Gonzalez, A.Aguila, L.Alonso-Mori, R.Barnes, C.O.Baxter, E.L.Brehmer, W.Brewster, A.S.Brunger, A.T.Calero, G.Chang, J.F.Chollet, M.Ehrensberger, P.Eriksson, T.L.Feng, Y.Hattne, J.Hedman, B.Hollenbeck, M.Holton, J.M.Keable, S.Kobilka, B.K.Kovaleva, E.G.Kruse, A.C.Lemke, H.T.Lin, G.Lyubimov, A.Y.Manglik, A.Mathews, I.I.McPhillips, S.E.Nelson, S.Peters, J.W.Sauter, N.K.Smith, C.A.Song, J.Stevenson, H.P.Tsai, Y.Uervirojnangkoorn, M.Vinetsky, V.Wakatsuki, S.Weis, W.I.Zadvornyy, O.A.Zeldin, O.B.Zhu, D.Hodgson, K.O.

(2014) Proc.Natl.Acad.Sci.USA 111: 17122-17127

  • DOI: 10.1073/pnas.1418733111

  • PubMed Abstract: 
  • The emerging method of femtosecond crystallography (FX) may extend the diffraction resolution accessible from small radiation-sensitive crystals and provides a means to determine catalytically accurate structures of acutely radiation-sensitive metall ...

    The emerging method of femtosecond crystallography (FX) may extend the diffraction resolution accessible from small radiation-sensitive crystals and provides a means to determine catalytically accurate structures of acutely radiation-sensitive metalloenzymes. Automated goniometer-based instrumentation developed for use at the Linac Coherent Light Source enabled efficient and flexible FX experiments to be performed on a variety of sample types. In the case of rod-shaped Cpl hydrogenase crystals, only five crystals and about 30 min of beam time were used to obtain the 125 still diffraction patterns used to produce a 1.6-Å resolution electron density map. For smaller crystals, high-density grids were used to increase sample throughput; 930 myoglobin crystals mounted at random orientation inside 32 grids were exposed, demonstrating the utility of this approach. Screening results from cryocooled crystals of β2-adrenoreceptor and an RNA polymerase II complex indicate the potential to extend the diffraction resolution obtainable from very radiation-sensitive samples beyond that possible with undulator-based synchrotron sources.


    Organizational Affiliation

    Molecular and Cellular Physiology, and Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305;,Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720; Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158; and.,Molecular and Cellular Physiology, and Structural Biology, and.,Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59715.,Stanford Synchrotron Radiation Lightsource.,Photon Science, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025; Structural Biology, and.,Molecular and Cellular Physiology, and.,Stanford Synchrotron Radiation Lightsource, HodgsonK@stanford.edu acohen@slac.stanford.edu.,Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261;,Stanford Synchrotron Radiation Lightsource, Departments of Chemistry.,Linac Coherent Light Source, and.,Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720;,Stanford Synchrotron Radiation Lightsource, Departments of Chemistry, HodgsonK@stanford.edu acohen@slac.stanford.edu.




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 2 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.36 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.159 
  • Space Group: P 6
  • Diffraction Data DOI: 
    10.15785/SBGRID/417 SBGrid
Unit Cell:
Length (Å)Angle (°)
a = 90.309α = 90.00
b = 90.309β = 90.00
c = 45.204γ = 120.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHENIXrefinement
MOLREPphasing
cctbx.xfeldata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-11-05
    Type: Initial release
  • Version 1.1: 2014-12-03
    Type: Database references
  • Version 1.2: 2014-12-17
    Type: Database references
  • Version 1.3: 2015-04-01
    Type: Other
  • Version 1.4: 2015-11-18
    Type: Data collection
  • Version 1.5: 2017-11-15
    Type: Data collection, Derived calculations, Refinement description
  • Version 1.6: 2018-11-28
    Type: Data collection