1JX4
Crystal Structure of a Y-family DNA Polymerase in a Ternary Complex with DNA Substrates and an Incoming Nucleotide
Experimental procedure
| Experimental method | MAD |
| Source type | SYNCHROTRON |
| Source details | NSLS BEAMLINE X9B |
| Synchrotron site | NSLS |
| Beamline | X9B |
| Temperature [K] | 100 |
| Detector technology | CCD |
| Collection date | 2001-06-01 |
| Detector | MARRESEARCH |
| Wavelength(s) | 0.9832 |
| Spacegroup name | P 21 21 2 |
| Unit cell lengths | 97.090, 102.820, 52.300 |
| Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
| Resolution | 500.000 - 1.700 |
| R-factor | 0.213 |
| Rwork | 0.213 |
| R-free | 0.22800 |
| Structure solution method | MAD |
| RMSD bond length | 0.017 |
| RMSD bond angle | 1.943 |
| Data reduction software | DENZO |
| Data scaling software | SCALEPACK |
| Phasing software | SOLVE |
| Refinement software | CNS (1.0) |
Data quality characteristics
| Overall | Outer shell | |
| Low resolution limit [Å] | 30.000 | 1.730 |
| High resolution limit [Å] | 1.700 | 1.700 |
| Rmerge | 0.040 | 0.554 * |
| Number of reflections | 57010 | |
| <I/σ(I)> | 33.7 | 2.2 |
| Completeness [%] | 97.6 | 98.4 |
| Redundancy | 5.04 | 4.34 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 7 | 20 * | 16% PEG 3350, 0.1 M Hepes (pH 7.0), 100 mM calcium acetate, 2.5% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystallization Reagents
| ID | crystal ID | solution ID | reagent name | concentration | details |
| 1 | 1 | 1 | PEG 3350 | ||
| 2 | 1 | 1 | Hepes (pH 7.0) | ||
| 3 | 1 | 1 | calcium acetate | ||
| 4 | 1 | 1 | glycerol |
Crystallization Reagents in Literatures
| ID | crystal ID | solution | reagent name | concentration (unit) | details |
| 1 | 1 | drop | ddATP | 1 (mM) | or ddGTP |
| 10 | 1 | reservoir | glycerol | 2.5 (%) | |
| 2 | 1 | drop | HEPES | 20 (mM) | |
| 3 | 1 | drop | 60 (mM) | ||
| 4 | 1 | drop | 5 (mM) | ||
| 5 | 1 | drop | dithiothreitol | 1.0 (mM) | |
| 6 | 1 | drop | protein | 8 (mg/ml) | |
| 7 | 1 | reservoir | PEG3350 | 16 (%) | |
| 8 | 1 | reservoir | HEPES | 0.1 (M) | |
| 9 | 1 | reservoir | calcium acetate | 100 (mM) |
