9D9K
Crystal structure of MurC from Pseudomonas aeruginosa in complex with inhibitor M17
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 8EWA |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 291 | 0.50 M ammonium sulfate, 0.1 M HEPES pH 7.5. PsaeA.00137.b.B5.PW37941 at 22.5 mg/mL. Overnight soak with 5mM compound M17 in 1.0 M ammonium sulfate, 0.1M Hepes 7.5. plate 14333 well B8 drop 1. Puck: PSL-1208, Cryo: 2.5M ammonium sulfate + 5mM M17 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
5.77 | 78.68 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 108.711 | α = 90 |
b = 108.711 | β = 90 |
c = 265.044 | γ = 90 |
Symmetry | |
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Space Group | I 41 2 2 |
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 9M | 2024-08-03 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS-II BEAMLINE 19-ID | 0.9786 | NSLS-II | 19-ID |
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 | 2.63 | 132.52 | 100 | 0.237 | 0.245 | 0.065 | 0.998 | 10.7 | 14 | 24139 |
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 | 2.63 | 2.7 | 100 | 3.104 | 3.211 | 0.815 | 0.657 | 15.1 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 2.63 | 68.56 | 1.33 | 24098 | 1246 | 99.92 | 0.2062 | 0.2047 | 0.2329 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 13.784 |
f_angle_d | 0.825 |
f_chiral_restr | 0.049 |
f_plane_restr | 0.008 |
f_bond_d | 0.007 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2296 |
Nucleic Acid Atoms | |
Solvent Atoms | 32 |
Heterogen Atoms | 102 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
Aimless | data scaling |
XDS | data reduction |
PHASER | phasing |