1MU7
Crystal Structure of a Human Tyrosyl-DNA Phosphodiesterase (Tdp1)-Tungstate Complex
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | SYNCHROTRON |
| Source details | APS BEAMLINE 19-ID |
| Synchrotron site | APS |
| Beamline | 19-ID |
| Temperature [K] | 113 |
| Detector technology | CCD |
| Collection date | 2002-02-26 |
| Detector | CUSTOM-MADE |
| Wavelength(s) | 0.9790 |
| Spacegroup name | P 21 21 21 |
| Unit cell lengths | 50.058, 105.276, 194.683 |
| Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
| Resolution | 100.000 * - 2.000 |
| R-factor | 0.209 |
| Rwork | 0.201 |
| R-free | 0.21800 |
| Structure solution method | MOLECULAR REPLACEMENT |
| Starting model (for MR) | 1jy1 |
| RMSD bond length | 0.015 |
| RMSD bond angle | 1.610 |
| Data reduction software | HKL-2000 |
| Data scaling software | SCALEPACK |
| Phasing software | AMoRE |
| Refinement software | REFMAC |
Data quality characteristics
| Overall | Outer shell | |
| Low resolution limit [Å] | 46.300 | 2.070 |
| High resolution limit [Å] | 2.000 | 2.000 |
| Rmerge | 0.112 * | 0.409 * |
| Number of reflections | 70186 * | |
| <I/σ(I)> | 9.24 | 2.18 |
| Completeness [%] | 99.0 | 92.7 |
| Redundancy | 6.58 |
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) |
