7FVS
Crystal Structure of S. aureus gyrase in complex with 4-[[1-[(1-chloro-6,7-dihydro-5H-cyclopenta[c]pyridin-6-yl)methyl]azetidin-3-yl]methylamino]-6-fluorochromen-2-one
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | SLS BEAMLINE X10SA |
Synchrotron site | SLS |
Beamline | X10SA |
Temperature [K] | 100 |
Detector technology | CCD |
Collection date | 2017-07-12 |
Detector | MARMOSAIC 225 mm CCD |
Wavelength(s) | 0.979150 |
Spacegroup name | P 61 |
Unit cell lengths | 92.915, 92.915, 407.576 |
Unit cell angles | 90.00, 90.00, 120.00 |
Refinement procedure
Resolution | 80.467 - 2.160 |
R-factor | 0.1908 |
Rwork | 0.185 |
R-free | 0.22050 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | inhouse model |
RMSD bond length | 0.012 |
RMSD bond angle | 1.012 |
Data reduction software | XDS |
Data scaling software | XSCALE |
Phasing software | PHASER |
Refinement software | PHENIX (1.12rc1_2801) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 80.470 | 80.467 | 2.220 |
High resolution limit [Å] | 2.160 | 9.660 | 2.160 |
Rmerge | 0.164 | 0.055 | 2.231 |
Rmeas | 0.171 | 0.058 | 2.333 |
Total number of observations | 1321495 | ||
Number of reflections | 105846 | 1228 | 7631 |
<I/σ(I)> | 11.15 | 32.16 | 1.09 |
Completeness [%] | 99.8 | 99 | 97.2 |
Redundancy | 12.485 | 12.154 | 11.395 |
CC(1/2) | 0.998 | 0.998 | 0.226 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.5 | 295 | microbatch under paraffin oil: 500 nL each of ternary complex and reservoir consisting of 14% PEG5000 MME, 100mM BisTris/HCl pH 5.5: ternary complex made by mixing 14.5mg/mL gyrase in 20mM HEPES/NaOH, pH7.0, 100mM Na2SO4, 3mM MnCl2, 0.5mM TCEP with twice the molar ratio of DNA duplex (5-AGCCGTAGGGCCCTACGGCT-3, 3-TCGGCATCCCGGGATGCCGA-5) and six times molar ratio of small molecule inhibitor. |