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 1.5 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

  • DOI: 10.1111/febs.12922

  • PubMed Abstract: 
  • In macromolecular crystallography, the agreement between observed and predicted structure factors (Rcryst and Rfree ) is seldom better than 20%. This is much larger than the estimate of experimental error (Rmerge ). The difference between Rcryst and ...

    In macromolecular crystallography, the agreement between observed and predicted structure factors (Rcryst and Rfree ) is seldom better than 20%. This is much larger than the estimate of experimental error (Rmerge ). The difference between Rcryst and Rmerge is the R-factor gap. There is no such gap in small-molecule crystallography, for which calculated structure factors are generally considered more accurate than the experimental measurements. Perhaps the true noise level of macromolecular data is higher than expected? Or is the gap caused by inaccurate phases that trap refined models in local minima? By generating simulated diffraction patterns using the program MLFSOM, and including every conceivable source of experimental error, we show that neither is the case. Processing our simulated data yielded values that were indistinguishable from those of real data for all crystallographic statistics except the final Rcryst and Rfree . These values decreased to 3.8% and 5.5% for simulated data, suggesting that the reason for high R-factors in macromolecular crystallography is neither experimental error nor phase bias, but rather an underlying inadequacy in the models used to explain our observations. The present inability to accurately represent the entire macromolecule with both its flexibility and its protein-solvent interface may be improved by synergies between small-angle X-ray scattering, computational chemistry and crystallography. The exciting implication of our finding is that macromolecular data contain substantial hidden and untapped potential to resolve ambiguities in the true nature of the nanoscale, a task that the second century of crystallography promises to fulfill.


    Organizational Affiliation

    Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA; Physical Biosciences Division, Lawrence Berkeley National Laboratory, CA, 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 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

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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
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACTdata extraction
Blu-Icedata collection
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01-GM105404
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP50-GM073210
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP50-GM082250
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United 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
  • Version 1.5: 2019-12-25
    Type: Author supporting evidence