1NOP
Crystal structure of human tyrosyl-DNA phosphodiesterase (Tdp1) in complex with vanadate, DNA and a human topoisomerase I-derived peptide
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | APS BEAMLINE 19-BM |
Synchrotron site | APS |
Beamline | 19-BM |
Temperature [K] | 100 |
Detector technology | CCD |
Collection date | 2002-08-16 |
Detector | CUSTOM-MADE |
Wavelength(s) | 1.0332 |
Spacegroup name | P 21 21 21 |
Unit cell lengths | 49.803, 104.719, 193.924 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 100.000 * - 2.300 |
R-factor | 0.2083 |
Rwork | 0.206 |
R-free | 0.25200 * |
Structure solution method | MOLECULAR REPLACEMENT |
RMSD bond length | 0.014 |
RMSD bond angle | 1.387 |
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] | 95.650 | 2.360 |
High resolution limit [Å] | 2.300 | 2.300 |
Rmerge | 0.085 * | 0.339 * |
Number of reflections | 41018 | |
<I/σ(I)> | 2.08 | |
Completeness [%] | 92.6 * | 61.9 |
Redundancy | 4.7 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.8 | 298 | PEG 3000, sodium chloride, spermine, HEPES, 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 | spermine | ||
4 | 1 | 1 | HEPES | ||
5 | 1 | 2 | PEG 3000 | ||
6 | 1 | 2 | NaCl |
Crystallization Reagents in Literatures
ID | crystal ID | solution | reagent name | concentration (unit) | details |
1 | 1 | drop | Tdp1 | 5.5 (mg/ml) | |
2 | 1 | drop | sodium orthovanadate | 3 (mM) | |
3 | 1 | drop | DNA | 5 (mM/l) | |
4 | 1 | drop | peptide | 20 (mM/l) | |
5 | 1 | reservoir | PEG3350 | 22 (%) | |
6 | 1 | reservoir | HEPES | 100 (mM) | pH7.8 |
7 | 1 | reservoir | 200 (mM) | ||
8 | 1 | reservoir | spermine | 10 (mM) |