5P3D
Automated refinement of diffraction data obtained from an endothiapepsin crystal treated with fragment 166
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 1 21 1 |
Unit cell lengths | 45.276, 73.095, 52.620 |
Unit cell angles | 90.00, 109.33, 90.00 |
Refinement procedure
Resolution | 42.725 - 1.180 |
R-factor | 0.1259 |
Rwork | 0.125 |
R-free | 0.14340 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 4y5l |
RMSD bond length | 0.006 |
RMSD bond angle | 1.216 |
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] | 42.725 | 1.250 | |
High resolution limit [Å] | 1.180 | 3.530 | 1.180 |
Rmerge | 0.040 | 0.030 | 0.171 |
Rmeas | 0.049 | 0.036 | 0.220 |
Total number of observations | 238554 | ||
Number of reflections | 96335 | 3453 | 12392 |
<I/σ(I)> | 13.36 | 36.63 | 3.78 |
Completeness [%] | 90.7 | 85 | 72.3 |
Redundancy | 2.476 | ||
CC(1/2) | 0.998 | 0.998 | 0.942 |
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 166 with the SMILES code C[C@H](OC(=O)C1=CC2=C(CCC2)S1)C(N)=O |