3MPL
Crystal Structure of Bordetella pertussis BvgS VFT2 domain (Double Mutant F375E/Q461E)
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | 7.5 | 293 | 0.085M HEPES (pH 7.5), 10% PEG 40000 (w/v), 6.8% ethylene glycol, 5% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.26 | 45.49 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 48.8 | α = 90 |
| b = 101.48 | β = 90 |
| c = 53.83 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 21 21 2 |
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 | MAR scanner 345 mm plate | 2009-12-17 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | ROTATING ANODE | BRUKER AXS MICROSTAR | |||
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym 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 | 2.1 | 20 | 94.1 | 0.084 | 20.74 | 6.97 | 15270 | ||||||||||||
| 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) | |||||||||||
| 2.1 | 2.23 | 99 | 0.242 | 6.89 | 6.83 | ||||||||||||||
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 | PDB ENTRY 3MPK | 2.1 | 20 | 14494 | 776 | 94.25 | 0.19068 | 0.18785 | 0.24528 | RANDOM | 25.46 | ||||||
| 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] | |
| -0.56 | 0.16 | 0.4 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 37.297 |
| r_dihedral_angle_4_deg | 17.752 |
| r_dihedral_angle_3_deg | 15.846 |
| r_dihedral_angle_1_deg | 6.662 |
| r_scangle_it | 4.764 |
| r_scbond_it | 2.986 |
| r_mcangle_it | 2.199 |
| r_angle_refined_deg | 1.846 |
| r_mcbond_it | 1.255 |
| r_chiral_restr | 0.135 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 1799 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 82 |
| Heterogen Atoms | 8 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| MAR345dtb | data collection |
| AMoRE | phasing |
| REFMAC | refinement |
| XDS | data reduction |
| XSCALE | data scaling |
