8OJ1
Crystal structure of the DNA binding domain of M. polymorpha Auxin Response Factor 2 (MpARF2) in complex with High Affinity DNA
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | ALBA BEAMLINE XALOC |
Synchrotron site | ALBA |
Beamline | XALOC |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2018-12-11 |
Detector | DECTRIS PILATUS 6M |
Wavelength(s) | 0.97926 |
Spacegroup name | I 21 21 21 |
Unit cell lengths | 79.911, 80.933, 146.623 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 70.860 - 2.570 |
R-factor | 0.2433 |
Rwork | 0.242 |
R-free | 0.25920 |
Structure solution method | MOLECULAR REPLACEMENT |
RMSD bond length | 0.003 |
RMSD bond angle | 0.539 |
Phasing software | PHASER |
Refinement software | PHENIX (1.19.2_4158) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 70.860 | 2.610 |
High resolution limit [Å] | 2.566 | 2.566 |
Rmerge | 0.063 | 1.449 |
Rmeas | 0.066 | |
Number of reflections | 15573 | 42 |
<I/σ(I)> | 20 | 1.5 |
Completeness [%] | 99.8 | |
Redundancy | 9.7 | |
CC(1/2) | 0.999 | 0.715 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | Required amount of DNA to 2:1 (protein:DNA) stoichiometry was diluted in [20 mM Tris (pH8.0), 500 mM NaCl, 20 mM DTT] and protein was added to final concentration of 5 mg/mL. Crystals of MpARF2-DBD:DNA were obtained in 100 mM Tris pH 7-9, 18-33% PEG2KMME, 18.5% Glycerol by the sitting-drop vapor-diffusion method at 18 deg. C, in drops of 1 uL + 1 uL (protein:reservoir). Crystals appeared in less than a week. Cryo-cooling in liquid nitrogen was carried out using a cryo-protecting solution containing reservoir solution supplemented with 10% glycerol. |