8DND
Crystal structure of Bothrops pirajai Piratoxin-I (PrTX-I) and synthetic inhibitor Varespladib (LY315920)
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | LNLS BEAMLINE W01B-MX2 |
Synchrotron site | LNLS |
Beamline | W01B-MX2 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2018-05-15 |
Detector | DECTRIS PILATUS 2M |
Wavelength(s) | 1.425 |
Spacegroup name | P 21 21 2 |
Unit cell lengths | 69.748, 72.660, 44.280 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 50.317 - 2.018 |
R-factor | 0.193 |
Rwork | 0.192 |
R-free | 0.21710 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 2q2j |
Data reduction software | XDS |
Data scaling software | Aimless (0.6.2) |
Phasing software | PHASER (2.8.0) |
Refinement software | PHENIX (1.13_2998) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 50.320 | 50.320 | 2.130 |
High resolution limit [Å] | 2.018 | 6.380 | 2.020 |
Rmerge | 0.109 | 0.047 | 0.664 |
Rmeas | 0.119 | 0.052 | 0.724 |
Rpim | 0.047 | 0.021 | 0.286 |
Total number of observations | 3313 | 13759 | |
Number of reflections | 15085 | 557 | 2188 |
<I/σ(I)> | 12.6 | 30 | 2.6 |
Completeness [%] | 97.9 | 99.7 | 100 |
Redundancy | 6.3 | 5.9 | 6.3 |
CC(1/2) | 0.998 | 0.999 | 0.826 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 8.5 | 293 | 30% w/v PEG 4000, 0.1 M Tris HCl pH 8.5 and 0.2 M lithium sulfate |