Peptide Nanotubes: A Crystallographic Approach
107
3.2 Characterization of Dipeptide II (VΔF)
3.2.1 Crystallization and Data Collection
The crystals of peptide II were grown by slow evaporation of peptide solution
in methanol and water mixture. Rod-shaped crystals suitable for x-ray diffraction,
appeared within 4–5 days. 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 15 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.
3.2.2 Structure Determination and Refinement
The structure solution was obtained by 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 0.061. After
assigning each peak to the corresponding element, isotropic refinement was carried
out using the computer program SHELXL97 (Sheldrick 1997). Two water molecules
were located in the electron density map. Anisotropic refinement was carried out for
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. The refinement converged at the agreement
factor of 4.63% shown in Table 4.
3.2.3 Molecular Dimensions
Figure 10 shows the conformation of dipeptide II (VF) 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 [Val] are in
agreement with the previously observed values for the geometry of peptide groups
107
3.2 Characterization of Dipeptide II (VΔF)
3.2.1 Crystallization and Data Collection
The crystals of peptide II were grown by slow evaporation of peptide solution
in methanol and water mixture. Rod-shaped crystals suitable for x-ray diffraction,
appeared within 4–5 days. 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 15 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.
3.2.2 Structure Determination and Refinement
The structure solution was obtained by 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 0.061. After
assigning each peak to the corresponding element, isotropic refinement was carried
out using the computer program SHELXL97 (Sheldrick 1997). Two water molecules
were located in the electron density map. Anisotropic refinement was carried out for
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. The refinement converged at the agreement
factor of 4.63% shown in Table 4.
3.2.3 Molecular Dimensions
Figure 10 shows the conformation of dipeptide II (VF) 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 [Val] are in
agreement with the previously observed values for the geometry of peptide groups