1RH0
Crystal structure of human Tyrosyl-DNA Phosphodiesterase complexed with vanadate, octopamine and trinucleotide GTT
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | ALS BEAMLINE 8.2.2 |
Synchrotron site | ALS |
Beamline | 8.2.2 |
Temperature [K] | 100 |
Detector technology | CCD |
Collection date | 2003-02-01 |
Detector | ADSC QUANTUM 4 |
Wavelength(s) | 0.9791 |
Spacegroup name | P 21 21 21 |
Unit cell lengths | 49.692, 104.750, 194.033 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 50.000 - 2.300 |
R-factor | 0.19052 |
Rwork | 0.188 |
R-free | 0.23900 * |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 1jy1 |
RMSD bond length | 0.011 |
RMSD bond angle | 1.241 |
Data reduction software | HKL-2000 |
Data scaling software | SCALEPACK |
Phasing software | AMoRE |
Refinement software | REFMAC (5.1.24) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 50.000 | 2.360 |
High resolution limit [Å] | 2.300 | 2.300 |
Rmerge | 0.118 * | 0.505 * |
Number of reflections | 46407 | |
<I/σ(I)> | 13.72 | 2.53 |
Completeness [%] | 99.1 | 50.5 |
Redundancy | 4.9 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.2 * | 298 | PEG 3000, NaCl, HEPES, spermine, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
Crystallization Reagents
ID | crystal ID | solution ID | reagent name | concentration | details |
1 | 1 | 1 | PEG 3000 | ||
2 | 1 | 1 | NaCl | ||
3 | 1 | 1 | HEPES | ||
4 | 1 | 1 | spermine | ||
5 | 1 | 1 | H2O | ||
6 | 1 | 2 | PEG 3000 | ||
7 | 1 | 2 | NaCl | ||
8 | 1 | 2 | H2O |
Crystallization Reagents in Literatures
ID | crystal ID | solution | reagent name | concentration (unit) | details |
1 | 1 | drop | protein | 6.5 (mg/ml) | |
2 | 1 | drop | 250 (mM) | ||
3 | 1 | drop | Tris | 15 (mM) | pH8.2 |
4 | 1 | drop | EDTA | 1 (mM) | |
5 | 1 | reservoir | PEG3000 | 19-21 (%) | |
6 | 1 | reservoir | 200 (mM) | ||
7 | 1 | reservoir | spermine | 10 (mM) | |
8 | 1 | reservoir | HEPES | 100 (mM) | or MOPS, pH7.8 |