8E5E
Crystal structure of double-stranded DNA deaminase toxin DddA in complex with DNA with the target cytosine flipped into the active site
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | APS BEAMLINE 24-ID-C |
Synchrotron site | APS |
Beamline | 24-ID-C |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2021-06-21 |
Detector | DECTRIS EIGER2 X 16M |
Wavelength(s) | 0.979180 |
Spacegroup name | P 61 2 2 |
Unit cell lengths | 62.950, 62.950, 237.078 |
Unit cell angles | 90.00, 90.00, 120.00 |
Refinement procedure
Resolution | 35.780 - 2.620 |
R-factor | 0.2428 |
Rwork | 0.242 |
R-free | 0.25800 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 6u08 |
RMSD bond angle | 23.112 |
Data reduction software | XDS |
Data scaling software | Aimless (0.5.32) |
Phasing software | PHASER |
Refinement software | PHENIX (1.20.1_4487) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 44.870 | 2.740 |
High resolution limit [Å] | 2.620 | 2.620 |
Rmerge | 0.150 | 1.762 |
Rmeas | 0.171 | 1.904 |
Rpim | 0.079 | 0.706 |
Total number of observations | 50693 | 7585 |
Number of reflections | 8887 | 1076 |
<I/σ(I)> | 45.6 | 1.4 |
Completeness [%] | 98.0 | |
Redundancy | 5.7 | 7 |
CC(1/2) | 0.979 | 0.589 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | 0.2 M magnesium chloride, 0.1 M Tris-HCl, pH 8.5, 25 % polyethylene glycol 3350 |