1MU9
Crystal Structure of a Human Tyrosyl-DNA Phosphodiesterase (Tdp1)-Vanadate Complex
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | ALS BEAMLINE 5.0.2 |
Synchrotron site | ALS |
Beamline | 5.0.2 |
Temperature [K] | 113 |
Detector technology | CCD |
Collection date | 2002-03-20 |
Detector | ADSC QUANTUM 4 |
Wavelength(s) | 1.400 |
Spacegroup name | P 21 21 21 |
Unit cell lengths | 50.028, 104.980, 194.297 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 100.000 * - 2.050 |
R-factor | 0.205 |
Rwork | 0.199 |
R-free | 0.21400 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 1jy1 |
RMSD bond length | 0.013 |
RMSD bond angle | 1.618 |
Data reduction software | DENZO |
Data scaling software | SCALEPACK |
Phasing software | AMoRE |
Refinement software | REFMAC |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 19.970 | 2.120 |
High resolution limit [Å] | 2.050 | 2.050 |
Rmerge | 0.105 | 0.387 * |
Number of reflections | 65167 * | |
<I/σ(I)> | 11.78 | |
Completeness [%] | 99.8 | 100 |
Redundancy | 6.62 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.2 * | 298 | PEG 8000, sodium chloride, HEPES, spermine, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
Crystallization Reagents in Literatures
ID | crystal ID | solution | reagent name | concentration (unit) | details |
1 | 1 | drop | 250 (mM) | ||
10 | 1 | reservoir | spermine | 10-15 (mM) | |
2 | 1 | drop | Tris-HCl | 15 (mM) | pH8.2 |
3 | 1 | drop | EDTA | 1 (mM) | |
4 | 1 | drop | TCEP | 2 (mM) | |
5 | 1 | drop | protein | 6.5 (mg/ml) | |
6 | 1 | reservoir | sodium orthovanadate | 5 (mM) | |
7 | 1 | reservoir | PEG3000 | 19-21 (%) | |
8 | 1 | reservoir | HEPES | 100 (mM) | pH7.8 |
9 | 1 | reservoir | 200 (mM) |