5P5D
Automated refinement of diffraction data obtained from an endothiapepsin crystal treated with fragment 238
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | BESSY BEAMLINE 14.1 |
Synchrotron site | BESSY |
Beamline | 14.1 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2013-04-04 |
Detector | DECTRIS PILATUS 6M |
Wavelength(s) | 0.918409 |
Spacegroup name | P 21 21 21 |
Unit cell lengths | 45.234, 72.616, 104.022 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 42.284 - 1.579 |
R-factor | 0.1494 |
Rwork | 0.147 |
R-free | 0.18700 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 4y5l |
RMSD bond length | 0.009 |
RMSD bond angle | 1.156 |
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] | 45.234 | 1.680 | |
High resolution limit [Å] | 1.580 | 4.710 | 1.580 |
Rmerge | 0.102 | 0.037 | 0.523 |
Rmeas | 0.110 | 0.040 | 0.565 |
Total number of observations | 340512 | ||
Number of reflections | 47742 | 1961 | 7593 |
<I/σ(I)> | 16.07 | 42.33 | 3.72 |
Completeness [%] | 99.8 | 99.4 | 99.4 |
Redundancy | 7.132 | ||
CC(1/2) | 0.998 | 0.999 | 0.894 |
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 238 with the SMILES code [O-][N+](=O)C1=CC=C(S1)C(=O)NC1CC1 |