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Questions and answers => General discussions (Q&As) => Topic started by: xiangjun on September 18, 2012, 10:32:15 pm

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Title: Data files for Table 3 of the standard base-reference frame article
Post by: xiangjun on September 18, 2012, 10:32:15 pm

Table 3 of the Olson et al. (2001) "standard base-reference frame article (http://x3dna.bio.columbia.edu/data/Olson01-jmb-base-reference-frame.pdf)" lists the mean values and standard deviations of base geometric parameters for high resolution A-DNA and B-DNA crystal structures, as shown below.

(http://ndbserver.rutgers.edu/images/archives/report/tsukuba/table3.jpg)

The selection criteria of the A- and B-DNA datasets have recently been reported in the thread "Datasets and scripts for reproducing Figure 5 of the 3DNA NAR03 paper (http://forum.x3dna.org/general-discussions/datasets-and-scripts-for-reproducing-figure-5-of-the-3dna-nar03-paper/msg1037/#msg1037)". For the sake for easy reference and completeness, here is the note again:

Quote

Selection Criteria:
   NDB ID: ad OR bd
   Classification: DNA
   Structure Description: Double Helix
   Conformation Type: A OR B
   No Drug, No Mismatch
   No Modifiers (Base/Sugar/Phosphate)
   Resolution better than 2.0 A
   =======================
   34 A-DNA and 27 B-DNA

For B-DNA, delete bd0012, bd0013 & bdf068 (following HMB)
   bd0001 bd0006_A
   bd0014: coordinates from PDB 463D
   bd0005 bd0016_A (with repeated atoms!)
   bd0018 bd0019 bdj017 bdj019 bdj025 bdj031 bdj036 bdj037 bdj051
   bdj052 bdj060 bdj061 
   bdj081 (Uses helix #1 with strands A and B. The other two are
           disordered)
   bdl001 bdl005 bdl020 bdl084
   bd0023_A  bd0029
   -------------------------- 27-3=24 structures

For A-DNA
   ad0002 ==> (ad0002_AB + ad0002_CD)
   ad0003 ad0004 adh008 adh010 adh0102 adh0103 adh0104 adh0105
   adh014 adh026 adh027 adh029 adh033 adh034 adh038 adh039 adh047
   adh070 adh078 adj0102 adj0103 adj0112 adj0113 adj022 adj049
   adj050 adj051 adj065 adj066 adj067 adj075 
   adl025 (suspicious! big Buckle, alternating Propeller)
   adl047 (with B-steps, not good either!)
   -------------------------- 34+1-2=33 structures

Outliers:
  A-DNA: ad0002_CD, steps 3-4,   bps 3-4-5
         ad0004,    steps 3-4-5, bps 3-4-5-6
  B-DNA: bdj025,    step 3,      bps 3-4
         bdj031,    step 3,      bps 3-4
         bdj037,    step 3,      bps 3-4

The six data files themselves are attached below; here the A- prefix is for A-DNA, and B- prefix for B-DNA:

• 'A-base-pair.dat' and 'B-base-pair.dat' contain the base-pair parameters in the order of Shear, Stretch, Stagger, Buckle, Propeller, and Opening.
• 'A-step-pars.dat' and 'B-step-pars.dat' contain the step parameters in the order of Shift, Slide, Rse, Tilt, Roll and Twist.
• 'A-heli-pars.dat' and 'B-heli-pars.dat' contain the helical parameters in the order of x-displacement, y-displacement, Helical rise, Inclination, Tip, and Helical twist.

While the Table content is derived from NDB entries with only Watson-Crick base pairs in A- and B-DNA duplexes, it serves as a reference for identifying/quantifying non-canonical (mismatched) pairs by taking advantage the base-pair parameters. This approach is rigorous in its description of the relative base geometry in a pair, and is distinct from and complement with the Leontis-Westhof classification scheme.

Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids

Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University