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

    Stanford Synchrotron Radiation Lightsource, 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
PHENIXrefinement
PDB_EXTRACTdata extraction
cctbx.xfeldata reduction
MOLREPphasing

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