6BZ0
1.83 Angstrom Resolution Crystal Structure of Dihydrolipoyl Dehydrogenase from Acinetobacter baumannii in Complex with FAD.
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 5.5 | 293 | Protein: 22.6 mg/ml, 0.5M Sodium chloride, 0.01M Tris HCl (pH 8.3); Screen: Classics II (G10), 0.2M Magnesium chloride, 0.1M Bis-Tris (pH 5.5), 25% (w/v) PEG 3350. |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.08 | 40.8 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 57.965 | α = 80.38 |
| b = 82.769 | β = 80.21 |
| c = 96.262 | γ = 89.49 |
| Symmetry | |
|---|---|
| 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 | CCD | MARMOSAIC 300 mm CCD | C(111) | 2017-10-17 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | APS BEAMLINE 21-ID-F | 0.97872 | APS | 21-ID-F |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym I (Observed) | Rrim I (All) | Rpim I (All) | 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 | 1.83 | 30 | 97.6 | 0.08 | 0.08 | 0.093 | 0.047 | 15.2 | 3.9 | 150403 | -3 | 25.1 | |||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||
| 1 | 1.83 | 1.86 | 96.2 | 0.803 | 0.803 | 0.928 | 0.466 | 0.696 | 2.1 | 4 | |||||||||
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 | 5U8U | 1.83 | 29.63 | 142099 | 7557 | 97.6 | 0.18125 | 0.17903 | 0.22202 | RANDOM | 31.82 | ||||||
| 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] | |
| 0.18 | 1.07 | 0.2 | 1.89 | -0.04 | -1.78 | |
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 31.745 |
| r_dihedral_angle_4_deg | 10.206 |
| r_dihedral_angle_3_deg | 9.84 |
| r_long_range_B_refined | 5.278 |
| r_long_range_B_other | 5.182 |
| r_dihedral_angle_1_deg | 3.103 |
| r_scangle_other | 2.712 |
| r_mcangle_it | 2.017 |
| r_mcangle_other | 2.017 |
| r_scbond_it | 1.679 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 14064 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 1234 |
| Heterogen Atoms | 225 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| HKL-3000 | data reduction |
| HKL-3000 | data scaling |
| MoRDa | phasing |
