1O1Z
Crystal structure of glycerophosphodiester phosphodiesterase (GDPD) (TM1621) from Thermotoga maritima at 1.60 A resolution
Experimental procedure
| Experimental method | MAD |
| Source type | SYNCHROTRON |
| Source details | APS BEAMLINE 19-BM |
| Synchrotron site | APS |
| Beamline | 19-BM |
| Temperature [K] | 100 |
| Detector technology | CCD |
| Collection date | 2002-10-26 |
| Detector | APS-1 |
| Wavelength(s) | 0.98011, 0.97938, 0.97918, 0.95671 |
| Spacegroup name | P 21 21 2 |
| Unit cell lengths | 132.410, 41.790, 51.720 |
| Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
| Resolution | 50.000 * - 1.600 |
| R-factor | 0.141 |
| Rwork | 0.139 |
| R-free | 0.18000 |
| Structure solution method | MAD |
| RMSD bond length | 0.012 |
| RMSD bond angle | 1.410 * |
| Data reduction software | DENZO |
| Data scaling software | SCALEPACK |
| Phasing software | SOLVE |
| Refinement software | REFMAC (5.1.955) |
Data quality characteristics
| Overall | Outer shell | |
| Low resolution limit [Å] | 50.000 | 1.660 |
| High resolution limit [Å] | 1.600 | 1.600 |
| Rmerge | 0.050 * | 0.196 * |
| Total number of observations | 255060 * | |
| Number of reflections | 38012 | |
| <I/σ(I)> | 62.01 | 10.06 |
| Completeness [%] | 100.0 | 95.3 |
| Redundancy | 6.71 | 3.51 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | Vapor diffusion * | 9.6 | 277 | 40% (v/v) PEG-600, 0.1M CHES pH 9.5, pH 9.6, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K, pH 9.60 |
Crystallization Reagents in Literatures
| ID | crystal ID | solution | reagent name | concentration (unit) | details |
| 1 | 1 | drop | Tris | 20 (mM) | pH7.9 |
| 2 | 1 | drop | 150 (mM) | ||
| 3 | 1 | drop | TCEP | 0.25 (mM) | |
| 4 | 1 | drop | protein | 20 (mg/ml) | |
| 5 | 1 | reservoir | PEG600 | 40 (%) | |
| 6 | 1 | reservoir | CHES | 0.1 (M) | pH9.6 |
