6MV0

CO-bound Sperm Whale Myoglobin, room temperature structure solved by serial 5degree oscillation crystallography


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.0 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: 10.1107/S2052252519001453
  • Primary Citation of Related Structures:  

  • 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 ...

    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

    Kavli Institute for Nanoscale Science, Cornell University, Ithaca, NY 14853, USA.,Departments of Biochemistry and Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,MacCHESS, Cornell University, Ithaca, NY 14853, USA.,Max Planck Institute for the Structure and Dynamics of Matter, Hamburg, Germany.,Departments of Chemistry and Physics, University of Toronto, Toronto, ON Canada.,Department of Physics, Cornell University, Ithaca, NY 14853, USA.




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: 1.97 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.199 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 37.030α = 90.00
b = 45.900β = 90.00
c = 82.910γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM-103485
National Science Foundation (United States)United StatesDMR-1332208

Revision History 

  • Version 1.0: 2019-03-27
    Type: Initial release