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) |
