Peptide Nanotubes: A Crystallographic Approach
101
3 Characterization of Dipeptides
3.1 Characterization of Dipeptide I (FΔF)
3.1.1 Crystallization and Data Collection
The crystals of peptide I were grown by slow evaporation of peptide solution in
acetic acid and water mixture. The suitable crystal was mounted on the glass fibre
and X-ray diffraction data were collected on a Bruker AXS SMART APEX CCD
diffractometer equipped with Mo K α radiation. Unit cell parameters and orientation
matrix were determined initially by collecting three sets of data collected at three
different settings (set1 ϕ = 0°, 2θ = −28°, ω = −28°; set2 ϕ =90°, 2θ = −28°,
ω = −28°; set3 ϕ = 0°, 2θ = 28°, ω = 28°), each data set consists of 50 frames
with ω-scan width of 0.3°. The diffraction data were acquired over a hemisphere of
reciprocal lattice space by three different settings of ϕ (ϕ = 0°, 90°, 180°) and keeping
detector at an angle of 2θ = −25°, with detector to crystal distance of 6.07 cm. For
each setting of ϕ, 606 diffraction image frames with ω-width of 0.3° and exposure
time of 20 s per fame were obtained. The data processing was done by reducing the
image frames to obtain the integrated intensities for each reflection and intensities
were corrected for Lorentz and polarization factors. The data processing was done
using the software SAINTV6.1 (Bruker 1998). The data sets were corrected for the
absorption effect by using software SADABS (Sheldrick 1996). Finally, the corrected
intensity data were used for the structure solution and refinement.
3.1.2 Structure Determination and Refinement
The structure solution was obtained using direct methods employed in SHELXS97
software (Sheldrick 1997). All the non-hydrogen atoms were located in the E-map
of the best solution with a combined figure of merit (CFOM) value 0.0405. After
assigning each peak to the corresponding element, isotropic refinement was carried out using the computer program SHELXL97 (Sheldrick 1997). The acetic acid
molecule was located in the electron density map. Anisotropic refinement was carried out for all non-hydrogen atoms after the convergence of isotropic refinement.
All hydrogen atoms were fixed using stereochemical criteria and during the refinement, they were allowed to ride on their parent atoms. Refinement converged at the
agreement factor of 3.92%, shown in Table 1.
3.1.3 Molecular Dimensions
Figure 6 shows the conformation of dipeptide I (FF) with residue labelling. The
molecular parameters of all non-hydrogen atoms are given in Appendix C. In general,
the bond lengths and bond angles of the coded amino acid [Phe] are in agreement
101
3 Characterization of Dipeptides
3.1 Characterization of Dipeptide I (FΔF)
3.1.1 Crystallization and Data Collection
The crystals of peptide I were grown by slow evaporation of peptide solution in
acetic acid and water mixture. The suitable crystal was mounted on the glass fibre
and X-ray diffraction data were collected on a Bruker AXS SMART APEX CCD
diffractometer equipped with Mo K α radiation. Unit cell parameters and orientation
matrix were determined initially by collecting three sets of data collected at three
different settings (set1 ϕ = 0°, 2θ = −28°, ω = −28°; set2 ϕ =90°, 2θ = −28°,
ω = −28°; set3 ϕ = 0°, 2θ = 28°, ω = 28°), each data set consists of 50 frames
with ω-scan width of 0.3°. The diffraction data were acquired over a hemisphere of
reciprocal lattice space by three different settings of ϕ (ϕ = 0°, 90°, 180°) and keeping
detector at an angle of 2θ = −25°, with detector to crystal distance of 6.07 cm. For
each setting of ϕ, 606 diffraction image frames with ω-width of 0.3° and exposure
time of 20 s per fame were obtained. The data processing was done by reducing the
image frames to obtain the integrated intensities for each reflection and intensities
were corrected for Lorentz and polarization factors. The data processing was done
using the software SAINTV6.1 (Bruker 1998). The data sets were corrected for the
absorption effect by using software SADABS (Sheldrick 1996). Finally, the corrected
intensity data were used for the structure solution and refinement.
3.1.2 Structure Determination and Refinement
The structure solution was obtained using direct methods employed in SHELXS97
software (Sheldrick 1997). All the non-hydrogen atoms were located in the E-map
of the best solution with a combined figure of merit (CFOM) value 0.0405. After
assigning each peak to the corresponding element, isotropic refinement was carried out using the computer program SHELXL97 (Sheldrick 1997). The acetic acid
molecule was located in the electron density map. Anisotropic refinement was carried out for all non-hydrogen atoms after the convergence of isotropic refinement.
All hydrogen atoms were fixed using stereochemical criteria and during the refinement, they were allowed to ride on their parent atoms. Refinement converged at the
agreement factor of 3.92%, shown in Table 1.
3.1.3 Molecular Dimensions
Figure 6 shows the conformation of dipeptide I (FF) with residue labelling. The
molecular parameters of all non-hydrogen atoms are given in Appendix C. In general,
the bond lengths and bond angles of the coded amino acid [Phe] are in agreement