1K3T
Structure of Glycosomal Glyceraldehyde-3-Phosphate Dehydrogenase from Trypanosoma cruzi Complexed with Chalepin, a Coumarin Derivative Inhibitor
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | ROTATING ANODE |
Source details | RIGAKU RU200 |
Temperature [K] | 100 |
Detector technology | IMAGE PLATE |
Collection date | 1998-07-30 |
Detector | RIGAKU RAXIS IIC |
Wavelength(s) | 1.54 |
Spacegroup name | P 1 21 1 |
Unit cell lengths | 82.080, 84.970, 105.240 |
Unit cell angles | 90.00, 96.32, 90.00 |
Refinement procedure
Resolution | 15.000 - 1.950 |
Rwork | 0.201 |
R-free | 0.28000 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | Holo-D-Glyceraldehyde-3-phosphate dehydrogenase from T. cruzi solved at 2.8 A resolution by Souza et al. FEBS Letters 424 (1998) 131-135. |
RMSD bond length | 0.150 |
RMSD bond angle | 3.100 * |
Data reduction software | DENZO |
Data scaling software | SCALEPACK |
Phasing software | AMoRE |
Refinement software | REFMAC |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 44.720 | 2.020 |
High resolution limit [Å] | 1.950 | 1.950 |
Rmerge | 0.107 | 0.483 |
Total number of observations | 195798 * | |
Number of reflections | 81630 | |
<I/σ(I)> | 6.78 | 1.1 |
Completeness [%] | 77.9 | 38.1 |
Redundancy | 2.4 | 1.6 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | Vapor diffusion * | 7.6 * | 22 * | 16% PEG 8000, 0.1M calcium acetate, 0.1M sodium cacodylate, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
Crystallization Reagents in Literatures
ID | crystal ID | solution | reagent name | concentration (unit) | details |
1 | 1 | drop | protein | 8 (mg/ml) | |
10 | 1 | drop | acetonitrile | 10 (%(v/v)) | |
11 | 1 | reservoir | sodium cacodylate | 0.1 (M) | pH6.9-7.1 |
12 | 1 | reservoir | calcium acetate | 0.1 (M) | |
13 | 1 | reservoir | PEG8000 | 16-18 (%) | |
2 | 1 | drop | TEA | 0.1 (M) | pH7.6 |
3 | 1 | drop | NAD+ | 1 (mM) | |
4 | 1 | drop | dithiothreitol | 1 (mM) | |
5 | 1 | drop | PMSF | 1 (mM) | |
6 | 1 | drop | EDTA | 1 (mM) | |
7 | 1 | drop | leupeptin | 0.001 (mM) | |
8 | 1 | drop | pepstatin pre-incubated | 0.001 (mM) | |
9 | 1 | drop | inhibitor | 5 (mM) |