7UI4
Crystal structure of the DNA preQ0 insertase DpdA
Experimental procedure
Experimental method | MAD |
Source type | SYNCHROTRON |
Source details | SSRL BEAMLINE BL14-1 |
Synchrotron site | SSRL |
Beamline | BL14-1 |
Temperature [K] | 100 |
Detector technology | CCD |
Collection date | 2017-06-10 |
Detector | MARMOSAIC 325 mm CCD |
Wavelength(s) | 1.28149, 0.98397, 1.28268 |
Spacegroup name | P 21 21 2 |
Unit cell lengths | 86.102, 141.768, 42.496 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 54.780 - 2.510 |
R-factor | 0.1322 |
Rwork | 0.130 |
R-free | 0.17850 |
Structure solution method | MAD |
RMSD bond length | 0.006 |
RMSD bond angle | 1.078 |
Data reduction software | XDS (vJan26, 2018) |
Data scaling software | Aimless (0.7.1) |
Phasing software | SOLVE (2.13) |
Refinement software | REFMAC (5.8.0222) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 73.590 | 73.590 | 2.650 |
High resolution limit [Å] | 2.510 | 7.940 | 2.510 |
Rmerge | 0.103 | 0.035 | 0.964 |
Rmeas | 0.107 | 0.036 | 1.025 |
Rpim | 0.029 | 0.010 | 0.341 |
Total number of observations | 207845 | 8251 | 11600 |
Number of reflections | 16179 | 683 | 1324 |
<I/σ(I)> | 21.8 | 55.8 | 2.3 |
Completeness [%] | 87.1 | 99.9 | 50.4 |
Redundancy | 12.8 | 12.1 | 8.8 |
CC(1/2) | 0.999 | 0.999 | 0.920 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | mixing 2 ul sample containing 4.0 mg/ml protein (81.5 uM), 0.5 mM guanine, 50 mM Tris (pH 7.5), 100 mM NaCl and 1 mM DTT with 3 ul reservoir solution containing 10% (w/v) polyethylene glycol (PEG) 8000, 8% (v/v) ethylene glycol (EG), 100 mM HEPES (pH 7.5), 0.1 mM ZnCl2, 3 mM reduced glutathione (GSH) and 3 mM oxidized glutathione (GSSG) |