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) |