9B1Q
Crystal Structure of human Tryptophan 2,3-dioxygenase in complex with PYN1 inhibitor
This is a non-PDB format compatible entry.
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | NSLS-II BEAMLINE 17-ID-2 |
Synchrotron site | NSLS-II |
Beamline | 17-ID-2 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2024-02-10 |
Detector | DECTRIS EIGER X 16M |
Wavelength(s) | 0.97934 |
Spacegroup name | P 21 21 2 |
Unit cell lengths | 142.959, 154.170, 88.277 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 34.291 - 2.624 |
Rwork | 0.202 |
R-free | 0.25830 |
Structure solution method | MOLECULAR REPLACEMENT |
RMSD bond length | 0.007 |
RMSD bond angle | 1.417 |
Data reduction software | autoPROC |
Data scaling software | STARANISO |
Phasing software | PHASER |
Refinement software | REFMAC (5.8.0425) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 34.291 | 34.291 | 2.997 |
High resolution limit [Å] | 2.624 | 8.960 | 2.624 |
Rmerge | 0.136 | 0.048 | 1.060 |
Rmeas | 0.148 | 0.053 | 1.142 |
Rpim | 0.058 | 0.022 | 0.420 |
Total number of observations | 203088 | 9063 | 11616 |
Number of reflections | 31809 | 1590 | 1590 |
<I/σ(I)> | 9.62 | 28.4 | 1.79 |
Completeness [%] | 93.7 | 99.1 | 77.1 |
Completeness (spherical) [%] | 53.8 | 99.1 | 8.3 |
Completeness (ellipsoidal) [%] | 93.7 | 99.1 | 77.1 |
Redundancy | 6.38 | 5.7 | 7.31 |
CC(1/2) | 0.998 | 0.998 | 0.647 |
Anomalous completeness (spherical) | 52.4 | 99.6 | 7.6 |
Anomalous completeness | 93.4 | 99.6 | 76.3 |
Anomalous redundancy | 3.4 | 3.3 | 3.9 |
CC(ano) | -0.177 | -0.298 | -0.009 |
|DANO|/σ(DANO) | 0.8 | 0.7 | 0.8 |
Diffraction limits | Principal axes of ellipsoid fitted to diffraction cut-off surface |
2.608 Å | 1.000, 1.000, 1.000 |
3.336 Å | 0.000, 0.000, 0.000 |
3.666 Å | 0.000, 0.000, 0.000 |
Criteria used in determination of diffraction limits | local <I/sigmaI> ≥ 1.2 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | MICROBATCH | 298 | 50 mM Sodium Citrate pH 5.6, 2.0% Tacsimate pH 5.0, 5.0% PEG 3350 |