1PJO
Crystal Structure of an RNA/DNA hybrid of HIV-1 PPT
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | SYNCHROTRON |
| Source details | NSLS BEAMLINE X8C |
| Synchrotron site | NSLS |
| Beamline | X8C |
| Temperature [K] | 123 |
| Detector technology | CCD |
| Collection date | 1999-10-27 |
| Detector | ADSC QUANTUM 4 |
| Wavelength(s) | 1.0720 |
| Spacegroup name | P 21 21 21 |
| Unit cell lengths | 25.595, 40.755, 45.740 |
| Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
| Resolution | 20.000 - 1.100 |
| Rwork | 0.117 |
| R-free | 0.15600 * |
| Structure solution method | MOLECULAR REPLACEMENT |
| Starting model (for MR) | NDB ID AH0001 |
| RMSD bond length | 0.019 |
| RMSD bond angle | 0.043 |
| Data reduction software | DENZO |
| Data scaling software | SCALEPACK |
| Phasing software | EPMR |
| Refinement software | SHELXL-97 |
Data quality characteristics
| Overall | Outer shell | |
| Low resolution limit [Å] | 20.000 | 1.130 |
| High resolution limit [Å] | 1.100 | 1.100 |
| Rmerge | 0.058 | 0.492 |
| Number of reflections | 18327 | |
| <I/σ(I)> | 33.7 | 4.06 |
| Completeness [%] | 97.0 | 74.6 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | Vapor diffusion * | 6.8 * | 278 | magnesium acetate, beta-octylglucoside, spermidine hydrochloride, cacodylate, 2-methyl,2,4-pentanediol, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 278K |
Crystallization Reagents
| ID | crystal ID | solution ID | reagent name | concentration | details |
| 1 | 1 | 1 | magensium acetate | ||
| 2 | 1 | 1 | cacodylate | ||
| 3 | 1 | 1 | beta-octylglucoside | ||
| 4 | 1 | 1 | spermidine HCl | ||
| 5 | 1 | 1 | 2-methyl,2,4-pentanediol | ||
| 6 | 1 | 2 | magensium acetate | ||
| 7 | 1 | 2 | 2-methyl,2,4-pentanediol |
Crystallization Reagents in Literatures
| ID | crystal ID | solution | reagent name | concentration (unit) | details |
| 1 | 1 | drop | hybrid duplex | 0.3 (mM) | |
| 2 | 1 | drop | calcium acetate | 12 (mM) | |
| 3 | 1 | drop | spermidine hydrochloride | 0.6 (mM) | pH6.8 |
| 4 | 1 | drop | beta-octyl-glycoside | 0.075 (%) | |
| 5 | 1 | drop | sodium cacodylate | 12 (mM) | pH6.8 |
| 6 | 1 | drop | MPD | 12 (%(v/v)) | |
| 7 | 1 | reservoir | MPD | 50 (%) |
