6OS6
Crystal structure of CymD prenyltransferase complexed with L-tryptophan and DMSPP
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 | 2019-03-01 |
Detector | DECTRIS EIGER X 16M |
Wavelength(s) | 0.97932 |
Spacegroup name | I 4 |
Unit cell lengths | 129.446, 129.446, 49.777 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 29.118 - 1.330 |
R-factor | 0.1665 |
Rwork | 0.166 |
R-free | 0.18090 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | Author used SWISS-MODEL server to generate a phasing model based on the protein sequence. SWISS-MODEL produced a phasing model based on PDB Entry 5JXM. Author used the polyALA version of the model for phasing. |
Data reduction software | XDS |
Data scaling software | Aimless (0.5.21) |
Phasing software | PHASER |
Refinement software | PHENIX (1.13_2998) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 29.120 | 29.120 | 1.360 |
High resolution limit [Å] | 1.330 | 5.940 | 1.330 |
Rmerge | 0.070 | 0.041 | 0.685 |
Rmeas | 0.075 | 0.044 | 0.739 |
Rpim | 0.027 | 0.016 | 0.275 |
Total number of observations | 708407 | 8190 | 47653 |
Number of reflections | 95021 | 1123 | 6812 |
<I/σ(I)> | 15 | 44.2 | 2.3 |
Completeness [%] | 99.8 | 99.2 | 97.3 |
Redundancy | 7.5 | 7.3 | 7 |
CC(1/2) | 0.999 | 0.998 | 0.806 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 294 | 1% (w/v) tryptone, 0.05 M HEPES-Na (pH 7.0), 12% PEG 3350 |