Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 15.45 kDa 
• Atom Count: 1102 
• Modelled Residue Count: 128 
• Deposited Residue Count: 129 
• Unique protein chains: 1

4N5R

Hen egg-white lysozyme phased using free-electron laser data

• PDB DOI: 10.2210/pdb4N5R/pdb

• Classification: HYDROLASE
• Organism(s): Gallus gallus
• Mutation(s): No 


• Deposited: 2013-10-10 Released: 2013-11-27 
• Deposition Author(s): Barends, T.R.M., Foucar, L., Botha, S., Doak, R.B., Shoeman, R.L., Nass, K., Koglin, J.E., Williams, G.J., Boutet, S., Messerschmidt, M., Schlichting, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.256 
• R-Value Work: 0.231 
• R-Value Observed: 0.232 

Literature

De novo protein crystal structure determination from X-ray free-electron laser data.

Barends, T.R., Foucar, L., Botha, S., Doak, R.B., Shoeman, R.L., Nass, K., Koglin, J.E., Williams, G.J., Boutet, S., Messerschmidt, M., Schlichting, I.

(2014) Nature 505: 244-247

• PubMed: 24270807 
• DOI: 10.1038/nature12773
• Primary Citation of Related Structures:  
  4N5R


• PubMed Abstract: 
  

The determination of protein crystal structures is hampered by the need for macroscopic crystals. X-ray free-electron lasers (FELs) provide extremely intense pulses of femtosecond duration, which allow data collection from nanometre- to micrometre-sized crystals in a 'diffraction-before-destruction' approach. So far, all protein structure determinations carried out using FELs have been based on previous knowledge of related, known structures. Here we show that X-ray FEL data can be used for de novo protein structure determination, that is, without previous knowledge about the structure. Using the emerging technique of serial femtosecond crystallography, we performed single-wavelength anomalous scattering measurements on microcrystals of the well-established model system lysozyme, in complex with a lanthanide compound. Using Monte-Carlo integration, we obtained high-quality diffraction intensities from which experimental phases could be determined, resulting in an experimental electron density map good enough for automated building of the protein structure. This demonstrates the feasibility of determining novel protein structures using FELs. We anticipate that serial femtosecond crystallography will become an important tool for the structure determination of proteins that are difficult to crystallize, such as membrane proteins.

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Organizational Affiliation: 

Max-Planck Institute for Medical Research, Jahnstrasse 29, D-69120 Heidelberg, Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysozyme C	A	129	Gallus gallus	Mutation(s): 0  Gene Names: LYZ EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus) Explore P00698  Go to UniProtKB:  P00698

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DO3	D [auth A], E [auth A]	10-((2R)-2-HYDROXYPROPYL)-1,4,7,10-TETRAAZACYCLODODECANE 1,4,7-TRIACETIC ACID C17 H32 N4 O7 IQUHNCOJRJBMSU-CQSZACIVSA-N
GD	B [auth A], C [auth A]	GADOLINIUM ATOM Gd UIWYJDYFSGRHKR-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.256 
• R-Value Work: 0.231 
• R-Value Observed: 0.232 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.1	α = 90
b = 79.1	β = 90
c = 39.2	γ = 90

Software Package:

Software Name	Purpose
DAQ	data collection
PHASER	phasing
REFMAC	refinement
CrystFEL	data reduction
CrystFEL	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-10-10 
• Released Date: 2013-11-27 
Deposition Author(s): Barends, T.R.M., Foucar, L., Botha, S., Doak, R.B., Shoeman, R.L., Nass, K., Koglin, J.E., Williams, G.J., Boutet, S., Messerschmidt, M., Schlichting, I.

Revision History  

• Version 1.0: 2013-11-27
  Type: Initial release
  
• Version 1.1: 2013-12-25
  Changes: Database references
• Version 1.2: 2014-01-01
  Changes: Database references
• Version 1.3: 2014-01-22
  Changes: Database references
• Version 1.4: 2018-02-14
  Changes: Data collection