considered reasonable quality structures [46]. Apart from resolution, R value , R free
and real-space R-value and real-value correlations are among the important
parameters to assess the quality of crystal structure as discussed by Brown et al., in
2007 [45].
Geometric parameters and quality of structure: Apart from diffraction quality
and structure refinement parameters, geometric and chemical parameters are equally
important to consider while assessing its quality [15]. Atomic positions in model,
planarity of peptide plane, stereoisomer of peptide bond, bond length, bond angle,
and torsions angles should be checked for an unnatural occurrence [15]. Since all
combinations of backbone torsions /–w cannot occur in proteins, only those pairs
which conform to the Ramachandran plot, thus number of /–w pairs in disallowed
regions of the Ramachandran plot which ideally should be zero, generally lesser
violation considered better structure, are used as a critical parameter for the quality
of the crystal/model structure as best practices.
Atomic occupancy and B-factor are among other important parameters to be
considered while assessing the quality of structure. Occupancy of an atom is the
fraction of molecules which occupy modeled position among all molecules in
crystal. An occupancy 0.0 means modeled positions not observed in crystal, and 1.0
means modeled position is present in all molecules in crystal [47]. If some residues
in crystal structure show more than one conformations in crystal structure, then
conformation with highest occupancy should be preferred. In case of ligands, the
occupancy is dependent on K d value, e.g., for a ligand with K d in range
10–100 mM, maximum achievable occupancy ranges 70–90% or 0.70–0.90 considering working ligand concentration <500 mM [48]. B-factor in theory represents
the amplitude of oscillation of the atom around equilibrium position. It quantifies
the dynamics of the atom; often, isotropic B-factors are reported in crystal structures; however, anisotropic B-factors may be reported in high-resolution structures.
For high-resolution structures, anisotropic atomic displacement parameter
(B-factor) can be substantiated only when resolution is higher than *1.4 Å [46].
Structural regions in crystal structure having B-factor higher than a threshold
B_max should be carefully inspected because of their implications to high disorder
in the region [49].
At times, in crystal structure water molecules play important role in binding and
have to be considered for characterizing the binding site for its water interaction
profiles [50]. However, identification of structurally important waters involved in
receptor–ligand interaction is another challenge [51, 52].
Proteins are usually flexible molecules, and inherent dynamics characterizes its
interaction. Moreover, a crystal structure is usually a time and space average of the
conformers present in the crystal lattice [15]. Therefore, quite often it may not be
the conformation presenting the best possible affinity for the given ligand due to the
rigid treatment of the receptor. Thus, protein should be allowed to flex in such way
that it could show best possible affinity with the ligand.
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S. K. Panday and I. Ghosh
and real-space R-value and real-value correlations are among the important
parameters to assess the quality of crystal structure as discussed by Brown et al., in
2007 [45].
Geometric parameters and quality of structure: Apart from diffraction quality
and structure refinement parameters, geometric and chemical parameters are equally
important to consider while assessing its quality [15]. Atomic positions in model,
planarity of peptide plane, stereoisomer of peptide bond, bond length, bond angle,
and torsions angles should be checked for an unnatural occurrence [15]. Since all
combinations of backbone torsions /–w cannot occur in proteins, only those pairs
which conform to the Ramachandran plot, thus number of /–w pairs in disallowed
regions of the Ramachandran plot which ideally should be zero, generally lesser
violation considered better structure, are used as a critical parameter for the quality
of the crystal/model structure as best practices.
Atomic occupancy and B-factor are among other important parameters to be
considered while assessing the quality of structure. Occupancy of an atom is the
fraction of molecules which occupy modeled position among all molecules in
crystal. An occupancy 0.0 means modeled positions not observed in crystal, and 1.0
means modeled position is present in all molecules in crystal [47]. If some residues
in crystal structure show more than one conformations in crystal structure, then
conformation with highest occupancy should be preferred. In case of ligands, the
occupancy is dependent on K d value, e.g., for a ligand with K d in range
10–100 mM, maximum achievable occupancy ranges 70–90% or 0.70–0.90 considering working ligand concentration <500 mM [48]. B-factor in theory represents
the amplitude of oscillation of the atom around equilibrium position. It quantifies
the dynamics of the atom; often, isotropic B-factors are reported in crystal structures; however, anisotropic B-factors may be reported in high-resolution structures.
For high-resolution structures, anisotropic atomic displacement parameter
(B-factor) can be substantiated only when resolution is higher than *1.4 Å [46].
Structural regions in crystal structure having B-factor higher than a threshold
B_max should be carefully inspected because of their implications to high disorder
in the region [49].
At times, in crystal structure water molecules play important role in binding and
have to be considered for characterizing the binding site for its water interaction
profiles [50]. However, identification of structurally important waters involved in
receptor–ligand interaction is another challenge [51, 52].
Proteins are usually flexible molecules, and inherent dynamics characterizes its
interaction. Moreover, a crystal structure is usually a time and space average of the
conformers present in the crystal lattice [15]. Therefore, quite often it may not be
the conformation presenting the best possible affinity for the given ligand due to the
rigid treatment of the receptor. Thus, protein should be allowed to flex in such way
that it could show best possible affinity with the ligand.
118
S. K. Panday and I. Ghosh