2LZT

REFINEMENT OF TRICLINIC LYSOZYME. II. THE METHOD OF STEREOCHEMICALLY RESTRAINED LEAST-SQUARES


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Refinement of triclinic lysozyme: II. The method of stereochemically restrained least squares.

Ramanadham, M.Sieker, L.C.Jensen, L.H.

(1990) Acta Crystallogr.,Sect.B 46: 63-69


  • PubMed Abstract: 
  • Refinement of triclinic lysozyme by restrained least squares against the 2 A resolution X-ray data is described, beginning with the model from cycle 17 of the preceding paper [Hodsdon, Brown, Sieker & Jensen (1990). Acta Cryst. B46, 54-62]. After 20 ...

    Refinement of triclinic lysozyme by restrained least squares against the 2 A resolution X-ray data is described, beginning with the model from cycle 17 of the preceding paper [Hodsdon, Brown, Sieker & Jensen (1990). Acta Cryst. B46, 54-62]. After 20 refinement cycles, R stood at 0.172. Nevertheless, serious errors involving both main-chain and side-chain atoms still remained, requiring numerous model rebuilding sessions interleaved with refinement cycles. After 63 cycles R = 0.124 for the model which includes all protein atoms, 249 water oxygen sites and five nitrate ions. Although the overall B is relatively low, 10.5 A2, B's for atoms in the region of residues 101-103, toward the termini of some of the longer side chains, and in the region of the C terminus of the main chain exceed 20 A2, indicating relatively high atomic mobilities, disorder, or remaining errors in the model.


    Related Citations: 
    • Srlsq Refinement of Triclinic Lysozyme
      Ramanadham, M.,Sieker, L.C.,Jensen, L.H.
      (1987) Acta Crystallogr.,Sect.A 43: 13
    • Structures of Triclinic Mono-and Di-N-Acetylglucosamine. Lysozyme Complexes-A Crystallographic Study
      Kurachi, K.,Sieker, L.C.,Jensen, L.H.
      (1976) J.Mol.Biol. 101: 11
    • Metal Ion Binding in Triclinic Lysozyme
      Kurachi, K.,Sieker, L.C.,Jensen, L.H.
      (1975) J.Biol.Chem. 250: 7663
    • Triclinic Lysozyme. Some Features of the Structure at 2 Angstroms Resolution
      Ramanadham, M.,Sieker, L.C.,Jensen, L.H.
      (1989) The Immune Response to Structurally Defined Proteins. The Lysozyme Model --: 15
    • Structure of Triclinic Lysozyme and its Cu2+ Complex at 2 Angstroms Resolution
      Ramanadham, M.,Sieker, L.C.,Jensen, L.H.
      (1981) Acta Crystallogr.,Sect.A 37: 33
    • Refinement of Triclinic Lysozyme. I. Fourier and Least Squares Methods
      Hodsdon, J.M.,Brown, G.M.,Sieker, L.C.,Jensen, L.H.
      () TO BE PUBLISHED --: --


    Organizational Affiliation

    Neutron Physics Division, Bhabha Atomic Research Centre, Trombay, Bombay, India.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HEN EGG WHITE LYSOZYME
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
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: 1.97 Å
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 27.283α = 88.53
b = 31.980β = 108.57
c = 34.291γ = 111.85
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1990-01-15
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance