7CI8
Crystal structure of P.aeruginosa LpxC in complex with inhibitor
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3UHM |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 8 | 293 | 20 % w/v Polyethylene glycol 6,000 100 mM Tris pH 8.0 200 mM Magnesium chloride |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.47 | 50.29 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 50.037 | α = 72.6 |
b = 50.264 | β = 76.97 |
c = 76.141 | γ = 64.6 |
Symmetry | |
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Space Group | P 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | IMAGE PLATE | RIGAKU RAXIS VII | 2016-11-24 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU MICROMAX-007 HF | 1.5418 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 3 | 26.73 | 96.7 | 0.173 | 5.2 | 3.83 | 12288 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 3 | 3.11 | 96.1 | 0.409 | 2.1 | 3.95 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 3UHM | 3 | 26.74 | 11659 | 626 | 96.54 | 0.27018 | 0.2657 | 0.35047 | RANDOM | 39.701 |
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] | |
0.26 | -0.14 | 0.04 | 0.13 | 0.09 | -0.44 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 30.907 |
r_dihedral_angle_4_deg | 19.804 |
r_dihedral_angle_3_deg | 19.37 |
r_long_range_B_refined | 6.785 |
r_long_range_B_other | 6.783 |
r_dihedral_angle_1_deg | 5.861 |
r_mcangle_it | 2.789 |
r_mcangle_other | 2.788 |
r_scangle_other | 2.25 |
r_mcbond_it | 1.638 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 4656 |
Nucleic Acid Atoms | |
Solvent Atoms | 70 |
Heterogen Atoms | 43 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
CrystalClear | data reduction |
CrystalClear | data scaling |
MOLREP | phasing |