7XDJ
Crystal structure of actinomycin D-echinomycin-d(AGCGCGT/ACGAGCT) complex
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | NSRRC BEAMLINE BL15A1 |
Synchrotron site | NSRRC |
Beamline | BL15A1 |
Temperature [K] | 100 |
Detector technology | CCD |
Collection date | 2018-04-23 |
Detector | RAYONIX MX300HE |
Wavelength(s) | 0.91982 |
Spacegroup name | H 3 |
Unit cell lengths | 132.522, 132.522, 49.595 |
Unit cell angles | 90.00, 90.00, 120.00 |
Refinement procedure
Resolution | 24.835 - 2.435 |
R-factor | 0.2043 |
Rwork | 0.201 |
R-free | 0.23630 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 7dq0 |
Data reduction software | HKL-2000 |
Data scaling software | HKL-2000 |
Phasing software | PHENIX (1.14_3260) |
Refinement software | PHENIX (1.14_3260) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 30.000 | 30.000 | 2.530 |
High resolution limit [Å] | 2.400 | 5.250 | 2.440 |
Rmerge | 0.084 | 0.058 | 0.759 |
Rmeas | 0.088 | 0.061 | 0.801 |
Rpim | 0.027 | 0.019 | 0.252 |
Number of reflections | 24192 | 1205 | 1216 |
<I/σ(I)> | 13.6 | ||
Completeness [%] | 99.8 | 99.6 | 98.1 |
Redundancy | 11.1 | 10.9 | 9.7 |
CC(1/2) | 0.999 | 0.849 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 293 | 0.25 mM Oligonucleotide, 0.25 mM Echinomycin, 0.125 mM Actinomycin D, 2.5 mM Sodium cacodylate, 3.5 mM Magnesium chloride, 1 mM Spermine tetrahydrochloride, 6 mM Cobalt chloride, 1% (v/v) 2-Methyl-2,4-pentanediol, 6% (v/v) PEG 200, Reservior PEG 200 (30%) |