5O41

Low-dose fixed target serial synchrotron crystallography structure of sperm whale myoglobin

• PDB DOI: https://doi.org/10.2210/pdb5O41/pdb
• Entry: 5O41 supersedes: 5M3R

• Classification: OXYGEN BINDING
• Organism(s): Physeter catodon
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2017-05-25 Released: 2017-06-14 
• Deposition Author(s): Owen, R.L., Axford, D., Sherrell, D., Mueller-Werkmeister, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.253 
• R-Value Work: 0.195 
• R-Value Observed: 0.201 

Literature

Low-dose fixed-target serial synchrotron crystallography.

Owen, R.L., Axford, D., Sherrell, D.A., Kuo, A., Ernst, O.P., Schulz, E.C., Miller, R.J., Mueller-Werkmeister, H.M.

(2017) Acta Crystallogr D Struct Biol 73: 373-378

• PubMed: 28375148 
• DOI: https://doi.org/10.1107/S2059798317002996
• Primary Citation of Related Structures:  
  5M3S, 5O41


• PubMed Abstract: 
  

  The development of serial crystallography has been driven by the sample requirements imposed by X-ray free-electron lasers. Serial techniques are now being exploited at synchrotrons. Using a fixed-target approach to high-throughput serial sampling, it is demonstrated that high-quality data can be collected from myoglobin crystals, allowing room-temperature, low-dose structure determination. The combination of fixed-target arrays and a fast, accurate translation system allows high-throughput serial data collection at high hit rates and with low sample consumption.

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Organizational Affiliation: 

Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 18.2 kDa 
• Atom Count: 1,484 
• Modelled Residue Count: 154 
• Deposited Residue Count: 154 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Myoglobin	A	154	Physeter catodon	Mutation(s): 1  Gene Names: MB
UniProt
Find proteins for P02185 (Physeter macrocephalus) Explore P02185  Go to UniProtKB:  P02185

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	B [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
SO4	C [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CMO	D [auth A]	CARBON MONOXIDE C O UGFAIRIUMAVXCW-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.253 
• R-Value Work: 0.195 
• R-Value Observed: 0.201 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.873	α = 90
b = 46.876	β = 90
c = 84.665	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DIALS	data reduction
cctbx.prime	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-06-14 
Deposition Author(s): Owen, R.L., Axford, D., Sherrell, D., Mueller-Werkmeister, H.
• This entry supersedes: 5M3R

Revision History  

• Version 1.0: 2017-06-14
  Type: Initial release
  
• Version 1.1: 2024-01-17
  Changes: Data collection, Database references, Refinement description