4ET9 | pdb_00004et9

Hen egg-white lysozyme solved from 5 fs free-electron laser pulse data

• PDB DOI: https://doi.org/10.2210/pdb4ET9/pdb

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


• Deposited: 2012-04-24 Released: 2012-06-13 
• Deposition Author(s): Boutet, S., Lomb, L., Williams, G., Barends, T., Aquila, A., Doak, R.B., Weierstall, U., DePonte, D., Steinbrener, J., Shoeman, R., Messerschmidt, M., Barty, A., White, T., Kassemeyer, S., Kirian, R., Seibert, M., Montanez, P., Kenney, C., Herbst, R., Hart, P., Pines, J., Haller, G., Gruner, S., Philllip, H., Tate, M., Hromalik, M., Koerner, L., van Bakel, N., Morse, J., Ghonsalves, W., Arnlund, D., Bogan, M., Calemann, C., Fromme, R., Hampton, C., Hunter, M., Johansson, L., Katona, G., Kupitz, C., Liang, M., Martin, A., Nass, K., Redecke, L., Stellato, F., Timneanu, N., Wang, D., Zatsepin, N., Schafer, D., Defever, K., Neutze, R., Fromme, P., Spence, J., Chapman, H., Schlichting, I.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.227 (Depositor), 0.226 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Literature

High-resolution protein structure determination by serial femtosecond crystallography.

Boutet, S., Lomb, L., Williams, G.J., Barends, T.R., Aquila, A., Doak, R.B., Weierstall, U., DePonte, D.P., Steinbrener, J., Shoeman, R.L., Messerschmidt, M., Barty, A., White, T.A., Kassemeyer, S., Kirian, R.A., Seibert, M.M., Montanez, P.A., Kenney, C., Herbst, R., Hart, P., Pines, J., Haller, G., Gruner, S.M., Philipp, H.T., Tate, M.W., Hromalik, M., Koerner, L.J., van Bakel, N., Morse, J., Ghonsalves, W., Arnlund, D., Bogan, M.J., Caleman, C., Fromme, R., Hampton, C.Y., Hunter, M.S., Johansson, L.C., Katona, G., Kupitz, C., Liang, M., Martin, A.V., Nass, K., Redecke, L., Stellato, F., Timneanu, N., Wang, D., Zatsepin, N.A., Schafer, D., Defever, J., Neutze, R., Fromme, P., Spence, J.C., Chapman, H.N., Schlichting, I.

(2012) Science 337: 362-364

• PubMed: 22653729 
• DOI: https://doi.org/10.1126/science.1217737
• Primary Citation Related Structures: 
  4ET8, 4ET9, 4ETA, 4ETB, 4ETC, 4ETD, 4ETE


• PubMed Abstract: 
  

  Structure determination of proteins and other macromolecules has historically required the growth of high-quality crystals sufficiently large to diffract x-rays efficiently while withstanding radiation damage. We applied serial femtosecond crystallography (SFX) using an x-ray free-electron laser (XFEL) to obtain high-resolution structural information from microcrystals (less than 1 micrometer by 1 micrometer by 3 micrometers) of the well-characterized model protein lysozyme. The agreement with synchrotron data demonstrates the immediate relevance of SFX for analyzing the structure of the large group of difficult-to-crystallize molecules.

---

Organizational Affiliation: 
• Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA. [e-mail]

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: 14.39 kDa 
• Atom Count: 1,090 
• Modeled Residue Count: 129 
• Deposited Residue Count: 129 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysozyme C	A	129	Gallus gallus	Mutation(s): 0  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
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	B [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.227 (Depositor), 0.226 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Diffraction Data: https://doi.org/10.11577/1096920

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79	α = 90
b = 79	β = 90
c = 38	γ = 90

Software Package:

Software Name	Purpose
CXI	data collection
PHENIX	model building
PHENIX	refinement
CrystFEL	data reduction
CrystFEL	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-06-13 
Deposition Author(s): Boutet, S., Lomb, L., Williams, G., Barends, T., Aquila, A., Doak, R.B., Weierstall, U., DePonte, D., Steinbrener, J., Shoeman, R., Messerschmidt, M., Barty, A., White, T., Kassemeyer, S., Kirian, R., Seibert, M., Montanez, P., Kenney, C., Herbst, R., Hart, P., Pines, J., Haller, G., Gruner, S., Philllip, H., Tate, M., Hromalik, M., Koerner, L., van Bakel, N., Morse, J., Ghonsalves, W., Arnlund, D., Bogan, M., Calemann, C., Fromme, R., Hampton, C., Hunter, M., Johansson, L., Katona, G., Kupitz, C., Liang, M., Martin, A., Nass, K., Redecke, L., Stellato, F., Timneanu, N., Wang, D., Zatsepin, N., Schafer, D., Defever, K., Neutze, R., Fromme, P., Spence, J., Chapman, H., Schlichting, I.

Revision History  

• Version 1.0: 2012-06-13
  Type: Initial release
  
• Version 1.1: 2012-08-08
  Changes: Database references
• Version 1.2: 2015-11-18
  Changes: Other
• Version 1.3: 2017-11-15
  Changes: Data collection
• Version 1.4: 2018-02-14
  Changes: Data collection
• Version 1.5: 2023-08-16
  Changes: Data collection, Database references, Derived calculations
• Version 1.6: 2024-11-27
  Changes: Structure summary