1B3T
EBNA-1 NUCLEAR PROTEIN/DNA COMPLEX
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | SYNCHROTRON |
| Source details | CHESS BEAMLINE F1 |
| Synchrotron site | CHESS |
| Beamline | F1 |
| Temperature [K] | 100 |
| Detector technology | CCD |
| Collection date | 1994-05-01 |
| Detector | CUSTOM-MADE |
| Spacegroup name | P 21 21 21 |
| Unit cell lengths | 60.083, 64.501, 111.938 |
| Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
| Resolution | 6.000 - 2.200 |
| R-factor | 0.208 |
| Rwork | 0.208 |
| R-free | 0.26800 |
| Structure solution method | MOLECULAR REPLACEMENT |
| Starting model (for MR) | 1vhi |
| RMSD bond length | 0.012 |
| RMSD bond angle | 1.700 |
| Data reduction software | DENZO |
| Data scaling software | SCALEPACK |
| Phasing software | X-PLOR |
| Refinement software | X-PLOR (3.843) |
Data quality characteristics
| Overall | Outer shell | |
| Low resolution limit [Å] | 20.000 | 2.180 |
| High resolution limit [Å] | 2.100 | 2.100 |
| Rmerge | 0.073 | 0.121 |
| Total number of observations | 142136 * | |
| Number of reflections | 25865 | |
| <I/σ(I)> | 4.5 | 3.1 |
| Completeness [%] | 98.9 | 74.5 * |
| Redundancy | 5.5 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 7.2 * | 277 | METHOD - HANGING DROP VAPOR DIFFUSION. RESERVOIR: 100 MM MES (PH 5.6) 20% PEG 4000, 500 MM NACL, 10 MM MGCL2, 10 MM DTT PROTEIN: 10MG/ML 1MM HEPES PH 7.2 1M NACL, 10 MM DTT DRY DNA RESUSPENDED IN THE PROTEIN CONTAINING SOLUTION IN MOLAR RATIO 1.5 (DSDNA) / 1.0 (EBNA1 DIMER) DROP: 50% PROTEIN/DNA SOLUTION 50% RESERVOIR SOLUTION CRYSTALLIZATION TEMPERATURE: 4 GEDREES C, vapor diffusion - hanging drop, temperature 277K |
Crystallization Reagents
| ID | crystal ID | solution ID | reagent name | concentration | details |
| 1 | 1 | 1 | HEPES | ||
| 10 | 1 | 2 | MGCL2 | ||
| 11 | 1 | 2 | DTT | ||
| 2 | 1 | 1 | NACL | ||
| 3 | 1 | 1 | DTT | ||
| 4 | 1 | 1 | PEG 4000 | ||
| 5 | 1 | 1 | MES | ||
| 6 | 1 | 1 | MGCL2 | ||
| 7 | 1 | 2 | PEG 4000 | ||
| 8 | 1 | 2 | MES | ||
| 9 | 1 | 2 | NACL |
Crystallization Reagents in Literatures
| ID | crystal ID | solution | reagent name | concentration (unit) | details |
| 1 | 1 | drop | EBNA | 10 (mg/ml) | |
| 10 | 1 | reservoir | dithiothreitol | 10 (mM) | |
| 2 | 1 | drop | HEPES | 1 (mM) | |
| 3 | 1 | drop | 1 (M) | ||
| 4 | 1 | drop | dithiothreitol | 10 (mM) | |
| 5 | 1 | drop | dsDNA | a ratio of 1.5 dsDNA molecules to EBNA1 dimer | |
| 6 | 1 | reservoir | MES | 100 (mM) | |
| 7 | 1 | reservoir | PEG4000 | 20 (%(v/v)) | |
| 8 | 1 | reservoir | 500 (mM) | ||
| 9 | 1 | reservoir | 10 (mM) |
