6Y6Z
Structure of Pseudomonas aeruginosa Penicillin-Binding Protein 3 (PBP3) in complex with Compound 1
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.8 | 294 | 25% (w/v) polyethylene glycol 3,350, 0.1M Bis-Tris propane pH 7.8 and 1% (w/v) protamine sulphate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.29 | 46.38 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 69.101 | α = 90 |
b = 83.142 | β = 90 |
c = 90.135 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 PILATUS 6M | mirrors | 2018-02-23 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04-1 | 0.9159 | Diamond | I04-1 |
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 | 1.7 | 61.113 | 95.3 | 0.16 | 0.178 | 0.076 | 0.998 | 4.3 | 5 | 44456 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 1.7 | 1.819 | 67.6 | 1.241 | 0.494 | 0.65 | 1.4 | 1.4 |
Refinement
Statistics | |||||||||||||||||||
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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 | 6HZR | 1.7 | 61.11 | 42331 | 2125 | 77.03 | 0.1779 | 0.1744 | 0.2496 | RANDOM | 28.026 |
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] | |
-7.41 | 2.25 | 5.16 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 29.845 |
r_dihedral_angle_4_deg | 18.666 |
r_rigid_bond_restr | 18.417 |
r_dihedral_angle_3_deg | 14.26 |
r_dihedral_angle_1_deg | 7.02 |
r_angle_refined_deg | 1.599 |
r_angle_other_deg | 1.332 |
r_chiral_restr | 0.076 |
r_bond_refined_d | 0.01 |
r_gen_planes_refined | 0.007 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3815 |
Nucleic Acid Atoms | |
Solvent Atoms | 301 |
Heterogen Atoms | 34 |
Software
Software | |
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Software Name | Purpose |
Aimless | data scaling |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
XDS | data reduction |
STARANISO | data scaling |