3NKB
A 1.9A crystal structure of the HDV ribozyme precleavage suggests both Lewis acid and general acid mechanisms contribute to phosphodiester cleavage
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | SYNCHROTRON |
| Source details | APS BEAMLINE 21-ID-F |
| Synchrotron site | APS |
| Beamline | 21-ID-F |
| Temperature [K] | 100 |
| Detector technology | CCD |
| Collection date | 2010-03-15 |
| Detector | MARMOSAIC 225 mm CCD |
| Wavelength(s) | 0.97872 |
| Spacegroup name | C 2 2 21 |
| Unit cell lengths | 64.837, 84.107, 102.020 |
| Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
| Resolution | 27.361 - 1.916 |
| R-factor | 0.2169 |
| Rwork | 0.214 |
| R-free | 0.24100 |
| Structure solution method | MOLECULAR REPLACEMENT |
| Starting model (for MR) | 1CX0 WITH PORTIONS OF P2 AND P4 DELETED |
| RMSD bond length | 0.003 |
| RMSD bond angle | 1.254 |
| Data reduction software | HKL-2000 |
| Data scaling software | HKL-2000 |
| Phasing software | PHASER |
| Refinement software | PHENIX (1.6_289) |
Data quality characteristics
| Overall | Outer shell | |
| Low resolution limit [Å] | 50.000 | 1.950 |
| High resolution limit [Å] | 1.900 | 1.900 |
| Number of reflections | 20583 | |
| <I/σ(I)> | 44.3 | 2.2 |
| Completeness [%] | 94.3 | 54.6 |
| Redundancy | 7.2 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 5 | 293 | 3.5 mg/mL RNA, 10 mM MgCl2, 50 mM potassium acetate, 1 mM spermine, 30% MPD, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
