Crystal Structure of LpxC from Pseudomonas aeruginosa complexed with the potent BB-78485 inhibitor
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 1P42 | PDB ENTRY 1P42 |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | PALPXC, 10 MG/ML IN 25 MM HEPES PH 7.0, 2 MM TCEP, 0.3 M NACL, 1MM ZNCL2. BB-78485 ADDED TO 1 MM. HANGING DROP, 0.1 M SODIUM CACODYLATE PH 6.5, 0.2 M AMMONIUM SULFATE AND 10 % PEG 8000, 10 MM ZNCL2. | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.13 | 50.32 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 90.542 | α = 90 |
| b = 103.331 | β = 90 |
| c = 105.284 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 21 21 21 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 173 | CCD | ADSC CCD | MIRRORS | 2004-12-01 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | APS BEAMLINE 17-ID | APS | 17-ID | |
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 | 1.9 | 34.15 | 99.9 | 0.08 | 23.61 | 6.4 | 78112 | ||||||||||||
| 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 | 1.9 | 1.97 | 99.5 | 0.52 | 2.5 | 5.7 | |||||||||||||
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 (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | ||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1P42 | 1.9 | 73.72 | 74089 | 3927 | 99.6 | 0.179 | 0.177 | 0.19 | 0.221 | 0.24 | RANDOM | 23.05 | ||||
| Temperature Factor Modeling | ||||||
|---|---|---|---|---|---|---|
| Anisotropic B[1][1] | Anisotropic B[2][2] | Anisotropic B[3][3] | ||||
| 0.75 | -0.83 | 0.08 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 33.124 |
| r_dihedral_angle_4_deg | 15.259 |
| r_dihedral_angle_3_deg | 12.611 |
| r_dihedral_angle_1_deg | 5.822 |
| r_scangle_it | 1.856 |
| r_scbond_it | 1.289 |
| r_angle_refined_deg | 1.122 |
| r_angle_other_deg | 1.024 |
| r_mcangle_it | 0.768 |
| r_mcbond_it | 0.67 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 6863 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 1223 |
| Heterogen Atoms | 107 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| MOLREP | phasing |
