9MP1
Crystal structure of mithramycin analogue MTM SA-7-methyl-Trp in complex with double-stranded DNA AGAGGCCTCT
This is a non-PDB format compatible entry.
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | SYNCHROTRON |
| Source details | NSLS-II BEAMLINE 19-ID |
| Synchrotron site | NSLS-II |
| Beamline | 19-ID |
| Temperature [K] | 100 |
| Detector technology | PIXEL |
| Collection date | 2023-12-08 |
| Detector | DECTRIS EIGER2 X 9M |
| Wavelength(s) | 0.975 |
| Spacegroup name | P 41 3 2 |
| Unit cell lengths | 94.184, 94.184, 94.184 |
| Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
| Resolution | 38.480 - 2.080 |
| R-factor | 0.2206 |
| Rwork | 0.219 |
| R-free | 0.24810 |
| Structure solution method | MOLECULAR REPLACEMENT |
| RMSD bond length | 0.005 |
| RMSD bond angle | 1.186 |
| Data reduction software | HKL-2000 |
| Data scaling software | HKL-2000 |
| Phasing software | PHASER |
| Refinement software | REFMAC (5.8.0267) |
Data quality characteristics
| Overall | Outer shell | |
| Low resolution limit [Å] | 50.000 | 2.120 |
| High resolution limit [Å] | 2.080 | 2.080 |
| Rmerge | 0.098 | |
| Number of reflections | 9078 | 434 |
| <I/σ(I)> | 47.9 | |
| Completeness [%] | 100.0 | 100 |
| Redundancy | 23.5 | 24.8 |
| CC(1/2) | 1.000 | 0.958 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 291 | Reservoir: 10-35% v/v 2-methyl-2,4-pentanediol Drop: 0.5 mM double-stranded DNA, 1.0 mM MTM analogue, 10 mM sodium cacodylate pH 6.0, 4 mM zinc acetate dihydrate and 2 mM spermine |
