1RFI
Crystal structure of human Tyrosyl-DNA Phosphodiesterase complexed with vanadate, pentapeptide KLNYK, and tetranucleotide AGTC
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 | 49.820, 104.832, 193.539 |
| Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
| Resolution | 50.000 - 2.200 |
| R-factor | 0.18977 |
| Rwork | 0.188 |
| R-free | 0.22700 * |
| Structure solution method | MOLECULAR REPLACEMENT |
| RMSD bond length | 0.010 |
| RMSD bond angle | 1.167 |
| 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 | 2.280 |
| High resolution limit [Å] | 2.200 | 2.200 |
| Rmerge | 0.125 * | 0.527 * |
| Number of reflections | 53356 | |
| <I/σ(I)> | 12.99 | 2.62 |
| Completeness [%] | 99.9 * | 99.8 |
| Redundancy | 5.26 |
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 |
