8C41
High resolution structure of the Streptococcus pneumoniae topoisomerase IV-DNA complex with the novel fluoroquinolone Delafloxacin
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3RAE |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 300 | 2.5% Tacsimate, 50 mM Na Cacodylate, 62.5 mM KCl, 7.5 mM MgCl2, 4-7.5% Isopropanol. 30% MPD as cryoprotectant |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.24 | 71 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 157.471 | α = 90 |
b = 157.471 | β = 90 |
c = 212.339 | γ = 120 |
Symmetry | |
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Space Group | P 31 2 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | PIXEL | DECTRIS EIGER2 XE 16M | 2022-10-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04 | 0.95373 | Diamond | I04 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Net I Over Average Sigma (I) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot | |||||
1 | 2.393 | 115.01 | 96.3 | 0.564 | 0.569 | 0.073 | 1 | 8.4 | 60.8 | 70836 | 2 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 2.394 | 2.689 | 84 | 4.363 | 4.483 | 0.62 | 0.83 | 1.8 | 49.5 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Work | R-Free | Mean Isotropic B | ||||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 2.393 | 115.01 | 70682 | 3458 | 58.857 | 0.195 | 0.1922 | 0.2432 | 51.207 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
-0.489 | -0.244 | -0.489 | 1.586 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_3_deg | 17.252 |
r_dihedral_angle_6_deg | 15.192 |
r_dihedral_angle_2_deg | 8.023 |
r_dihedral_angle_1_deg | 7.653 |
r_lrange_it | 6.982 |
r_lrange_other | 6.972 |
r_mcangle_it | 4.711 |
r_mcangle_other | 4.71 |
r_scangle_it | 4.067 |
r_scangle_other | 4.067 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 11462 |
Nucleic Acid Atoms | 732 |
Solvent Atoms | 418 |
Heterogen Atoms | 92 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PDB-REDO | refinement |
DIALS | data reduction |
xia2 | data reduction |
Aimless | data scaling |
STARANISO | data scaling |
PHASER | phasing |