4TWS

Gadolinium Derivative of Tetragonal Hen Egg-White Lysozyme at 1.45 A Resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.161 
  • R-Value Work: 0.138 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

The R-factor gap in macromolecular crystallography: an untapped potential for insights on accurate structures.

Holton, J.M.Classen, S.Frankel, K.A.Tainer, J.A.

(2014) Febs J. 281: 4046-4060


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysozyme C
A
129Gallus gallusGene 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 4 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
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 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: 1.45 Å
  • R-Value Free: 0.161 
  • R-Value Work: 0.138 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 77.220α = 90.00
b = 77.220β = 90.00
c = 38.810γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHENIXrefinement
Blu-Icedata collection
XSCALEdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01-GM105404
National Institutes of Health/National Institute of General Medical SciencesUnited StatesP50-GM073210
National Institutes of Health/National Institute of General Medical SciencesUnited StatesP50-GM082250
National Institutes of Health/National Institute of General Medical SciencesUnited StatesU54-GM094625

Revision History 

  • Version 1.0: 2014-08-20
    Type: Initial release
  • Version 1.1: 2014-10-01
    Type: Database references
  • Version 1.2: 2016-08-03
    Type: Derived calculations, Structure summary
  • Version 1.3: 2017-09-13
    Type: Author supporting evidence, Derived calculations
  • Version 1.4: 2017-11-22
    Type: Refinement description