1M6F
Strong Binding in the DNA Minor Groove by an Aromatic Diamidine With a Shape That Does Not Match the Curvature of the Groove
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | ROTATING ANODE |
Source details | RIGAKU RU200 |
Temperature [K] | 104 |
Detector technology | IMAGE PLATE |
Collection date | 2002-06-27 |
Detector | RIGAKU RAXIS IV |
Wavelength(s) | 1.5418 |
Spacegroup name | P 21 21 21 |
Unit cell lengths | 24.098, 39.821, 65.620 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 10.000 - 1.780 |
R-factor | 0.1988 * |
Rwork | 0.202 |
R-free | 0.27130 * |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | DNA PART OF NDB ENTRY GDL009 |
RMSD bond length | 0.008 |
RMSD bond angle | 0.020 |
Data scaling software | SCALEPACK |
Phasing software | X-PLOR |
Refinement software | SHELXL-97 |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 17.000 | 1.840 |
High resolution limit [Å] | 1.780 | 1.780 |
Rmerge | 0.047 | 0.184 |
Total number of observations | 53082 * | |
Number of reflections | 6040 | |
Completeness [%] | 92.8 | 90.6 |
Redundancy | 8.8 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 285 | MGCL2 2UL OF 75MM, DNA DOUBLE-STRANDED 3UL OF 2MM, MPD 2UL OF 25%, DRUG 2UL OF 4.5MM, SODIUM CACODYLATE 40MM. MPD IN RESERVOIR 700UL OF 50%., pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K |
Crystallization Reagents
ID | crystal ID | solution ID | reagent name | concentration | details |
1 | 1 | 1 | MGCL2 | ||
2 | 1 | 1 | DNA | ||
3 | 1 | 1 | MPD | ||
4 | 1 | 1 | DRUG | ||
5 | 1 | 2 | MPD |
Crystallization Reagents in Literatures
ID | crystal ID | solution | reagent name | concentration (unit) | details |
1 | 1 | drop | 75 (mM) | ||
2 | 1 | drop | dsDNA | 2 (mM) | |
3 | 1 | drop | 25 (%(v/v)) | ||
4 | 1 | drop | CGP40215A compound | 4.5 (mM) | |
5 | 1 | drop | sodium cacodylate | 40 (mM) | pH6.5 |
6 | 1 | reservoir | MPD | 50 (%(v/v)) |