5OER

Hen egg-white lysozyme refined against 5000 9 keV diffraction patterns


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Multi-wavelength anomalous diffraction de novo phasing using a two-colour X-ray free-electron laser with wide tunability.

Gorel, A.Motomura, K.Fukuzawa, H.Doak, R.B.Grunbein, M.L.Hilpert, M.Inoue, I.Kloos, M.Kovacsova, G.Nango, E.Nass, K.Roome, C.M.Shoeman, R.L.Tanaka, R.Tono, K.Joti, Y.Yabashi, M.Iwata, S.Foucar, L.Ueda, K.Barends, T.R.M.Schlichting, I.

(2017) Nat Commun 8: 1170-1170

  • DOI: 10.1038/s41467-017-00754-7

  • PubMed Abstract: 
  • Serial femtosecond crystallography at X-ray free-electron lasers (XFELs) offers unprecedented possibilities for macromolecular structure determination of systems prone to radiation damage. However, de novo structure determination, i.e., without prior ...

    Serial femtosecond crystallography at X-ray free-electron lasers (XFELs) offers unprecedented possibilities for macromolecular structure determination of systems prone to radiation damage. However, de novo structure determination, i.e., without prior structural knowledge, is complicated by the inherent inaccuracy of serial femtosecond crystallography data. By its very nature, serial femtosecond crystallography data collection entails shot-to-shot fluctuations in X-ray wavelength and intensity as well as variations in crystal size and quality that must be averaged out. Hence, to obtain accurate diffraction intensities for de novo phasing, large numbers of diffraction patterns are required, and, concomitantly large volumes of sample and long X-ray free-electron laser beamtimes. Here we show that serial femtosecond crystallography data collected using simultaneous two-colour X-ray free-electron laser pulses can be used for multiple wavelength anomalous dispersion phasing. The phase angle determination is significantly more accurate than for single-colour phasing. We anticipate that two-colour multiple wavelength anomalous dispersion phasing will enhance structure determination of difficult-to-phase proteins at X-ray free-electron lasers.


    Organizational Affiliation

    Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, Heidelberg, 69120, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysozyme C
A
129Gallus gallusMutation(s): 0 
Gene Names: LYZ
EC: 3.2.1.17
Find proteins for P00698 (Gallus gallus)
Go to Gene View: LYZ
Go to UniProtKB:  P00698
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
DO3
Query on DO3

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Download CCD File 
A
10-((2R)-2-HYDROXYPROPYL)-1,4,7,10-TETRAAZACYCLODODECANE 1,4,7-TRIACETIC ACID
C17 H32 N4 O7
IQUHNCOJRJBMSU-CQSZACIVSA-N
 Ligand Interaction
GD
Query on GD

Download SDF File 
Download CCD File 
A
GADOLINIUM ATOM
Gd
UIWYJDYFSGRHKR-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.186 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 79.100α = 90.00
b = 79.100β = 90.00
c = 39.200γ = 90.00
Software Package:
Software NamePurpose
autoSHARPphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-10-25
    Type: Initial release
  • Version 1.1: 2017-11-01
    Type: Database references
  • Version 1.2: 2017-11-08
    Type: Database references
  • Version 1.3: 2018-01-24
    Type: Data collection
  • Version 1.4: 2018-11-14
    Type: Data collection