How the structure of lysozyme was actually determined

Blake, C. C. F.; Fenn, R. H.; Johnson, L. N.; Koenig, D. F.; Mair, G. A.; North, A. C. T.; Oldham, J. W. H.; Phillips, D. C.; Poljak, R. J.; Sarma, V. R.; Vernon, C. A.

doi:10.1107/97809553602060000899

International Tables for Crystallography (2012). Vol. F. ch. 25.1, pp. 845-872 | 1 | 2 |
https://doi.org/10.1107/97809553602060000899

Chapter 25.1. How the structure of lysozyme was actually determined

25.1. How the structure of lysozyme was actually determined (pp. 845-872) | html | pdf | chapter contents |
C. C. F. Blake, R. H. Fenn, L. N. Johnson, D. F. Koenig, G. A. Mair, A. C. T. North, J. W. H. Oldham, D. C. Phillips, R. J. Poljak, V. R. Sarma and C. A. Vernon
- 25.1.1. Introduction (p. 845) | html | pdf |
- 25.1.2. Structure analysis at 6 Å resolution (pp. 845-854) | html | pdf |
  - 25.1.2.1. Technical facilities (p. 845) | html | pdf |
  - 25.1.2.2. Lysozyme crystallization (p. 846) | html | pdf |
  - 25.1.2.3. Preparation of heavy-atom derivatives (pp. 846-847) | html | pdf |
  - 25.1.2.4. Determination of heavy-atom positions (pp. 847-848) | html | pdf |
    - 25.1.2.4.1. The mercuri-iodide (K₂HgI₄) derivative (p. 847) | html | pdf |
    - 25.1.2.4.2. The palladium chloride (K₂PdCl₄) derivative (p. 847) | html | pdf |
    - 25.1.2.4.3. The o-mercurihydroxytoluene p-sulfonate (MHTS) derivative (p. 847) | html | pdf |
    - 25.1.2.4.4. Other potential derivatives (pp. 847-848) | html | pdf |
  - 25.1.2.5. Refinement of heavy-atom parameters (p. 848) | html | pdf |
  - 25.1.2.6. Analysis in three dimensions (pp. 848-852) | html | pdf |
    - 25.1.2.6.1. X-ray intensity measurements (pp. 848-850) | html | pdf |
    - 25.1.2.6.2. Data processing (pp. 850-851) | html | pdf |
    - 25.1.2.6.3. The absolute scale of the intensities (p. 851) | html | pdf |
    - 25.1.2.6.4. Re-assessment of heavy-atom derivatives (pp. 851-852) | html | pdf |
  - 25.1.2.7. Phase determination at 6 Å resolution (p. 852) | html | pdf |
  - 25.1.2.8. The electron-density map of lysozyme at 6 Å resolution (pp. 853-854) | html | pdf |
- 25.1.3. Analysis of the structure at 2 Å resolution (pp. 854-866) | html | pdf |
  - 25.1.3.1. Heavy-atom derivatives at 2 Å resolution (pp. 855-856) | html | pdf |
  - 25.1.3.2. Intensity measurements (pp. 856-858) | html | pdf |
  - 25.1.3.3. The second low-resolution map at 6 Å (p. 858) | html | pdf |
  - 25.1.3.4. Intensity measurements at high resolution (pp. 858-859) | html | pdf |
    - 25.1.3.4.1. Experimental methods (pp. 858-859) | html | pdf |
    - 25.1.3.4.2. Diffractometer output (p. 859) | html | pdf |
  - 25.1.3.5. Data processing (pp. 859-860) | html | pdf |
    - 25.1.3.5.1. Absorption corrections (p. 860) | html | pdf |
  - 25.1.3.6. Further stages of data processing (pp. 860-861) | html | pdf |
  - 25.1.3.7. The crystal-type problem (pp. 861-862) | html | pdf |
  - 25.1.3.8. Final refinement of heavy-atom parameters (p. 862) | html | pdf |
  - 25.1.3.9. Calculation of phase values (pp. 862-863) | html | pdf |
  - 25.1.3.10. The electron-density map at 2 Å resolution (pp. 863-864) | html | pdf |
  - 25.1.3.11. Map interpretation and model building (pp. 864-866) | html | pdf |
- 25.1.4. Structural studies on the biological function of lysozyme (pp. 866-871) | html | pdf |
  - 25.1.4.1. Lysozyme substrates (p. 866) | html | pdf |
  - 25.1.4.2. The crystal structure of GlcNAc (pp. 866-867) | html | pdf |
  - 25.1.4.3. Low-resolution binding studies of lysozyme with GlcNAc and other sugars (p. 867) | html | pdf |
  - 25.1.4.4. Binding studies of lysozyme with tri-N-acetyl-chitotriose, (GlcNAc)₃, at 2 Å resolution (pp. 867-868) | html | pdf |
  - 25.1.4.5. Proposals for the catalytic mechanism of lysozyme (pp. 868-871) | html | pdf |
- References | html | pdf |
- Figures
  - Fig. 25.1.2.10. Phase determination for reflection 424 (p. 852) | html | pdf |
  - Fig. 25.1.2.11. Electron-density difference syntheses showing the main sites of substitution and subsidiary sites with low occupancy in the PdCl₄ and MHTS derivatives (Fenn, 1964) (p. 853) | html | pdf |
  - Fig. 25.1.2.12. Electron-density distribution in lysozyme at 6 Å resolution viewed parallel to the c axis (p. 853) | html | pdf |
  - Fig. 25.1.2.13. Views of a 6 Å resolution model of the regions in which the electron density exceeds about 0.53 e Å⁻³ (p. 854) | html | pdf |
  - Fig. 25.1.2.1. Tetragonal lysozyme crystals with well developed {110} faces (left-hand crystal) and small {110} faces (right-hand crystal) (p. 846) | html | pdf |
  - Fig. 25.1.2.2. Difference-Patterson h0l projection map for the derivative obtained with K₂PdCl₄ (p. 847) | html | pdf |
  - Fig. 25.1.2.3. Difference-Patterson hk0 projection for the derivative obtained with MHTS (p. 847) | html | pdf |
  - Fig. 25.1.2.4. Reciprocal-space diagrams showing the direction of the incident X-ray beam, the Ewald sphere and the genesis of a reflection (a) in an equatorial plane and (b) in the equi-inclination setting (p. 848) | html | pdf |
  - Fig. 25.1.2.5. Crystal mounting (p. 849) | html | pdf |
  - Fig. 25.1.2.6. Absorption curve (p. 850) | html | pdf |
  - Fig. 25.1.2.7. Typical output from the linear diffractometer (p. 850) | html | pdf |
  - Fig. 25.1.2.8. Format of monitor output in which the computer lists reflections that fail the tests for format or significance (p. 850) | html | pdf |
  - Fig. 25.1.2.9. Three-dimensional $[|\Delta F|^{2}]$ syntheses for the PdCl₄ and MHTS derivatives (p. 851) | html | pdf |
  - Fig. 25.1.3.10. The amino-acid sequence of hen egg-white lysozyme (Canfield & Liu, 1965) (p. 864) | html | pdf |
  - Fig. 25.1.3.11. Schematic drawing of the main-chain conformation of lysozyme (p. 865) | html | pdf |
  - Fig. 25.1.3.12. Stereo-photographs of a model of the lysozyme molecule to a scale of 2 cm to 1 Å (p. 865) | html | pdf |
  - Fig. 25.1.3.1. Perspective drawing of the sphere of reflection showing inclination geometry with simultaneous reflections (reciprocal-lattice points P and Q) from levels symmetrically related by the flat-cone setting (p. 857) | html | pdf |
  - Fig. 25.1.3.2. The $[a^{*}b^{*}]$ plane of the reciprocal lattice oriented to rotate about the $[[\bar{1}10]]$ axis (p. 857) | html | pdf |
  - Fig. 25.1.3.3. Solid model of the electron density greater than about 0.5 e Å⁻³ in the second study of lysozyme at 6 Å resolution (p. 858) | html | pdf |
  - Fig. 25.1.3.4. Paper-tape output from the triple-counter linear diffractometer, showing the indices of the central reflection and the background, peak, background counts for the three reflections (p. 859) | html | pdf |
  - Fig. 25.1.3.5. Asymmetric mounting of a protein crystal with its mother liquor in a capillary tube (p. 860) | html | pdf |
  - Fig. 25.1.3.6. Plot of the ratio $[\textstyle\sum_{h}\displaystyle I(h)/ \textstyle\sum_{h}\displaystyle I(-h)]$ against h (p. 860) | html | pdf |
  - Fig. 25.1.3.7. (a) Phase probability curve for a Bijvoet pair of reflections (broken lines) with the joint probability curve (full line) derived by the method of Blow & Rossmann (1961) (p. 863) | html | pdf |
  - Fig. 25.1.3.8. Variation of the mean figure of $[\langle m\rangle]$ with $[\sin^{2}\theta / \lambda^{2}]$ (crosses represent acentric reflections, open circles represent centric reflections) (p. 863) | html | pdf |
  - Fig. 25.1.3.9. Photograph of sections z = 35/60 to 44/60 of the three-dimensional electron-density map of hen egg-white lysozyme at 2 Å resolution (p. 864) | html | pdf |
  - Fig. 25.1.4.1. The cell-wall tetrasaccharide with the $[\beta (1\!\rightarrow \!4)]$ glycosidic bond that is hydrolysed by lysozyme indicated (Blake et al., 1967) (p. 866) | html | pdf |
  - Fig. 25.1.4.2. Inhibitor molecules of lysozyme (Blake et al., 1967) (p. 867) | html | pdf |
  - Fig. 25.1.4.3. Contemporary drawings of the binding to lysozyme of: (a) β-N-acetylglucosamine and (b) α-N-acetylglucosamine (Blake et al., 1967) (p. 869) | html | pdf |
  - Fig. 25.1.4.4. Stereo-photographs of a model of the lysozyme molecule showing how a hexasaccharide substrate may bind to the enzyme (p. 869) | html | pdf |
  - Fig. 25.1.4.5. Draft sketch of the lysozyme–hexasaccharide substrate complex prepared by Irving Geis and annotated by David Phillips for an article published in Scientific American in 1966 (Phillips, 1966) (p. 870) | html | pdf |
- Tables
  - Table 25.1.2.1. Heavy-atom parameters used in the final phase calculation for the lysozyme structure (p. 852) | html | pdf |
  - Table 25.1.3.1. Structure amplitudes of the $[11_{\prime}11_{\prime}L]$ reflections from crystal types I and II (p. 861) | html | pdf |
  - Table 25.1.3.2. Heavy-atom parameters for the 2 Å structure (p. 862) | html | pdf |
  - Table 25.1.3.3. Discrepancies in amino-acid sequences (excluding Asp/Asn) (p. 865) | html | pdf |

Chapter 25.1. How the structure of lysozyme was actually determined

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