Crystal structure of the Streptococcus pyogenes fibronectin binding protein Fbab-B
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | 8.5 | 2.47 - 2.52M AMMONIUM SULFATE, 0.26M MAGNESIUM ACETATE OR 0.21M MAGNESIUM CHLORIDE, 0.1M BICINE PH 8.5 - 9.5. CRYSTAL WAS CRYOPROTECTED DIRECTLY IN THIS SOLUTION SUPPLEMENTED WITH 25% GLYCEROL. | ||
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.38 | 48.4 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 57.22 | α = 90 |
| b = 57.22 | β = 90 |
| c = 64.58 | γ = 120 |
| Symmetry | |
|---|---|
| Space Group | P 61 |
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 | ADSC QUANTUM 315r | MIRRORS | 2008-05-17 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ESRF BEAMLINE ID29 | ESRF | ID29 | |
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 | 1.6 | 1.64 | 98.2 | 0.06 | 22 | 2.9 | 15019 | ||||||||||||
| 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 | 1.6 | 1.64 | 96.7 | 0.43 | 3.4 | 1.9 | |||||||||||||
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 | SAD | THROUGHOUT | NONE | 1.6 | 27.06 | 15019 | 789 | 99.8 | 0.138 | 0.136 | 0.15 | 0.17 | 0.18 | RANDOM | 16.74 | ||||
| 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] | |
| 0.05 | 0.03 | 0.05 | -0.08 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 37.252 |
| r_dihedral_angle_3_deg | 12.34 |
| r_dihedral_angle_4_deg | 10.974 |
| r_sphericity_free | 8.762 |
| r_dihedral_angle_1_deg | 6.189 |
| r_sphericity_bonded | 4.757 |
| r_rigid_bond_restr | 4.308 |
| r_scangle_it | 4.001 |
| r_scbond_it | 2.56 |
| r_mcangle_it | 1.822 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 779 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 103 |
| Heterogen Atoms | |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| XDS | data reduction |
| XSCALE | data scaling |
| SHELXCDE | phasing |
