6D6F

Triclinic lysozyme cryocooled to 100 K with 47% xylose as cryoprotectant

  • Classification: HYDROLASE
  • Organism(s): Gallus gallus

  • Deposited: 2018-04-20 Released: 2018-09-19 
  • Deposition Author(s): Juers, D.H.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.137 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The impact of cryosolution thermal contraction on proteins and protein crystals: volumes, conformation and order.

Juers, D.H.Farley, C.A.Saxby, C.P.Cotter, R.A.Cahn, J.K.B.Holton-Burke, R.C.Harrison, K.Wu, Z.

(2018) Acta Crystallogr D Struct Biol 74: 922-938

  • DOI: 10.1107/S2059798318008793
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Cryocooling of macromolecular crystals is commonly employed to limit radiation damage during X-ray diffraction data collection. However, cooling itself affects macromolecular conformation and often damages crystals via poorly understood processes. He ...

    Cryocooling of macromolecular crystals is commonly employed to limit radiation damage during X-ray diffraction data collection. However, cooling itself affects macromolecular conformation and often damages crystals via poorly understood processes. Here, the effects of cryosolution thermal contraction on macromolecular conformation and crystal order in crystals ranging from 32 to 67% solvent content are systematically investigated. It is found that the solution thermal contraction affects macromolecule configurations and volumes, unit-cell volumes, crystal packing and crystal order. The effects occur through not only thermal contraction, but also pressure caused by the mismatched contraction of cryosolvent and pores. Higher solvent-content crystals are more affected. In some cases the solvent contraction can be adjusted to reduce mosaicity and increase the strength of diffraction. Ice formation in some crystals is found to cause damage via a reduction in unit-cell volume, which is interpreted through solvent transport out of unit cells during cooling. The results point to more deductive approaches to cryoprotection optimization by adjusting the cryosolution composition to reduce thermal contraction-induced stresses in the crystal with cooling.


    Organizational Affiliation

    Program in BBMB, Whitman College, 345 Boyer Avenue, Walla Walla, WA 99362, USA.,Department of Physics, Whitman College, 345 Boyer Avenue, Walla Walla, WA 99362, 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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
XYS
Query on XYS

Download SDF File 
Download CCD File 
A
XYLOPYRANOSE
C5 H10 O5
SRBFZHDQGSBBOR-LECHCGJUSA-N
 Ligand Interaction
NO3
Query on NO3

Download SDF File 
Download CCD File 
A
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.137 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 26.956α = 88.23
b = 31.864β = 71.54
c = 33.991γ = 68.51
Software Package:
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
CrysalisProdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-04-20 
  • Released Date: 2018-09-19 
  • Deposition Author(s): Juers, D.H.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States2R15GM090248

Revision History 

  • Version 1.0: 2018-09-19
    Type: Initial release
  • Version 1.1: 2018-10-31
    Type: Data collection, Database references
  • Version 1.2: 2020-01-01
    Type: Author supporting evidence, Data collection