Introduction

 

The Nucleic Acid Database Project [1] was created in 1991 as a resource for reseachers in the field of nucleic acid structure. Beginning in January 1996, the NDB also became a deposition site for oligonucleotide crystal structures. The purpose of the NDB is to gather all structural information about oligonucleotides obtained from x-ray crystallographic experiments, and to organize this information in a manner that maximizes the utility of this information for the diverse community of consumers and producers of nucleic acid structure data.

Table 1 shows the distribution of the 440 crystal structures in the NDB as of July 1996. The NDB includes coordinate data as well as information describing the crystallographic experiment and refinement. Structural features derived from coordinate data such as bond distances, angles, torsions and base morphology are calculated for each structure and included in the NDB. The primary and derived data in the NDB are summarized in Tables 2 and 3.

 

Structure Type Number

A-DNA 57

B-DNA 76

Z-DNA 52

DNA-Drug Complexes 98

DNA/RNA Hybrid 15

A-RNA 13

RNA-Drug Complexes 19

t-RNA 10

DNA with unusual features 21

RNA with unusual feature 16

Protein-DNA complexes 67

Protein-RNA complexes 8

 

Structure features Descriptor NDB, PDB and CSD identifiers Availability of coordinates Availability of structure factors

Structure description Sequence Conformation type Description of modifiers of base, phosphate and sugar Mismatched base-pairs Name and binding type for drug Description of base pairing Description of asymmetric unit Description of the biological unit

Citation Authors Title Journal Volume Pages Year

Crystal data Cell dimensions Space group

Data collection description Source of radiation Data collection device Radiation wavelength Temperature Resolution range Total number of unique reflections

Crystallization description Method Temperature pH value Composition of solutions BMCD crystal identifier

Refinement information Method Program Number of reflections used for refinement Data cutoff Resolution range R-factor Refinement of temperature factors and occupancies

Coordinate information Atomic coordinates, occupancies and temperature factors for the asymmetric unit Symmetry operations to generate the unit cell Symmetry operations to generate the biological unit

 

Distances Covalent bond lengths Nonbonded contacts Virtual bonds involving phosphorus atoms

Torsions Backbone and side chain torsion angles Pseudorotation parameters

Angles Valence bond angles Virtual angles involving phosphorus atoms

Base morphology Parameters calculated by a variety of algorithms

RMS deviations Deviations and RMS deviations from small molecule standard values for covalent bond distances and angles.