Chapter 7. Model Building and Refinement

  1. Dr. Albrecht Messerschmidt

Published Online: 5 JAN 2007

DOI: 10.1002/9783527610129.ch7

X-Ray Crystallography of Biomacromolecules: A Practical Guide

X-Ray Crystallography of Biomacromolecules: A Practical Guide

How to Cite

Messerschmidt, A. (2007) Model Building and Refinement, in X-Ray Crystallography of Biomacromolecules: A Practical Guide, Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim, Germany. doi: 10.1002/9783527610129.ch7

Author Information

  1. Max-Planck-Institue of Biochemistry, Department of Proteomics and Signal Transduction, Research Group: Structural Proteomics, Am Klopferspitz 18, 82152 Martinsried, Germany

Publication History

  1. Published Online: 5 JAN 2007
  2. Published Print: 15 DEC 2007

ISBN Information

Print ISBN: 9783527313969

Online ISBN: 9783527610129

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Keywords:

  • model building;
  • crystallographic refinement;
  • principles of least squares;
  • refinement by simulated annealing;
  • refinement at atomic resolution;
  • verification and accuracy of structure determination;
  • determination of coordinate uncertainty;
  • validation;
  • protein data bank

Summary

This chapter contains sections titled:

  • Model Building

  • Crystallographic Refinement

    • Introduction

    • Principles of Least Squares

    • Constraints and Restraints in Refinement

    • Refinement by Simulated Annealing

    • The Maximum Likelihood Method

    • Refinement at Atomic Resolution

  • Verification and Accuracy of Structure Determination

    • Free R-Factor as a Tool for Cross-Validation in Structure Determination

    • Determination of Coordinate Uncertainty

      • Unrestrained Least-Squares Refinement

      • Restrained Least-Squares Refinement

      • Rough Estimation of Coordinate Uncertainties

        • Luzzati Plot

        • σA-Plot

        • The Diffraction-Component Precision Index

    • Validation of the Geometric and Stereochemical Parameters of the Structural Model

    • Validation of the Structural Model against the Experimental Data

    • Deposition of Structural Data with the Protein Data Bank