5P8D
Automated refinement of diffraction data obtained from an endothiapepsin crystal treated with fragment 346
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | BESSY BEAMLINE 14.3 |
Synchrotron site | BESSY |
Beamline | 14.3 |
Temperature [K] | 100 |
Detector technology | CCD |
Collection date | 2014-01-22 |
Detector | MAR CCD 165 mm |
Wavelength(s) | 0.8944 |
Spacegroup name | P 1 21 1 |
Unit cell lengths | 45.363, 73.149, 52.964 |
Unit cell angles | 90.00, 109.57, 90.00 |
Refinement procedure
Resolution | 20.975 - 1.179 |
R-factor | 0.1282 |
Rwork | 0.127 |
R-free | 0.14350 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 4y5l |
RMSD bond length | 0.006 |
RMSD bond angle | 1.218 |
Data reduction software | XDS |
Data scaling software | XDS |
Phasing software | PHASER (2.5.7) |
Refinement software | PHENIX |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 42.741 | 1.250 | |
High resolution limit [Å] | 1.180 | 3.530 | 1.180 |
Rmerge | 0.049 | 0.022 | 0.410 |
Rmeas | 0.057 | 0.026 | 0.474 |
Total number of observations | 438046 | ||
Number of reflections | 106825 | 4065 | 17056 |
<I/σ(I)> | 16.33 | 48.49 | 3.32 |
Completeness [%] | 99.7 | 98.9 | 99 |
Redundancy | 4.1 | ||
CC(1/2) | 0.999 | 0.999 | 0.868 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 4.6 | 290 | 0.1 M ammonium acetate, 0.1 M sodium acetate, 24-30% PEG 4000; crystal obtained by streak-seeding and soaked with 90 mM of fragment 346 with the SMILES code FC(F)(F)C1=NN=C2C=CC(NC3CC3)=NN12 |