4Z98

Crystal Structure of Hen Egg White Lysozyme using Serial X-ray Diffraction Data Collection


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

A high-transparency, micro-patternable chip for X-ray diffraction analysis of microcrystals under native growth conditions.

Murray, T.D.Lyubimov, A.Y.Ogata, C.M.Vo, H.Uervirojnangkoorn, M.Brunger, A.T.Berger, J.M.

(2015) Acta Crystallogr. D Biol. Crystallogr. 71: 1987-1997

  • DOI: 10.1107/S1399004715015011

  • PubMed Abstract: 
  • Microcrystals present a significant impediment to the determination of macromolecular structures by X-ray diffraction methods. Although microfocus synchrotron beamlines and X-ray free-electron lasers (XFELs) can enable the collection of interpretable ...

    Microcrystals present a significant impediment to the determination of macromolecular structures by X-ray diffraction methods. Although microfocus synchrotron beamlines and X-ray free-electron lasers (XFELs) can enable the collection of interpretable diffraction data from microcrystals, there is a need for efficient methods of harvesting small volumes (<2 µl) of microcrystals grown under common laboratory formats and delivering them to an X-ray beam source under native growth conditions. One approach that shows promise in overcoming the challenges intrinsic to microcrystal analysis is to pair so-called `fixed-target' sample-delivery devices with microbeam-based X-ray diffraction methods. However, to record weak diffraction patterns it is necessary to fabricate devices from X-ray-transparent materials that minimize background scattering. Presented here is the design of a new micro-diffraction device consisting of three layers fabricated from silicon nitride, photoresist and polyimide film. The chip features low X-ray scattering and X-ray absorption properties, and uses a customizable blend of hydrophobic and hydrophilic surface patterns to help localize microcrystals to defined regions. Microcrystals in their native growth conditions can be loaded into the chips with a standard pipette, allowing data collection at room temperature. Diffraction data collected from hen egg-white lysozyme microcrystals (10-15 µm) loaded into the chips yielded a complete, high-resolution (<1.6 Å) data set sufficient to determine a high-quality structure by molecular replacement. The features of the chip allow the rapid and user-friendly analysis of microcrystals grown under virtually any laboratory format at microfocus synchrotron beamlines and XFELs.


    Organizational Affiliation

    Departments of Molecular and Cellular Physiology, Neurology and Neurological Sciences, Structural Biology and Photon Science, and Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA.,Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA.,Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Biophysics Graduate Group, University of California, Berkeley, CA 94720, USA.,GM/CA@APS, X-Ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA.




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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.205 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 79.144α = 90.00
b = 79.144β = 90.00
c = 38.111γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
Cootmodel building
cctbx.xfeldata reduction
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
HCIAUnited States--

Revision History 

  • Version 1.0: 2015-10-14
    Type: Initial release
  • Version 1.1: 2018-05-16
    Type: Data collection, Database references, Derived calculations