Room temperature X-ray structure of the B1 domain of streptococcal protein G triple mutant T2Q, N8D, and N37D (GB1-QDD).
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 9I2I | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | MICRODIALYSIS | 278 | 50 % 2-methyl-2,4-pentanediol (MPD), 25 % isopropanol | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.44 | 49.6 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 78.699 | α = 90 |
| b = 35.409 | β = 122.6 |
| c = 51.82 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | C 1 2 1 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 295 | PIXEL | DECTRIS EIGER2 X CdTe 9M | 2025-10-30 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ESRF BEAMLINE ID30B | 0.95372 | ESRF | ID30B |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | 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 | 1.69 | 31.23 | 97.1 | 0.073 | 0.97 | 9.1 | 5.5 | 13158 | 16.84 | ||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
| 1 | 1.69 | 1.72 | 0.264 | 0.4 | 4.7 | 5.1 | |||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | 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) | Mean Isotropic B | |||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 1.69 | 31.23 | 1.36 | 13157 | 675 | 96.57 | 0.1683 | 0.1666 | 0.1668 | 0.1967 | 0.1969 | 24.46 | |||||
| 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] | |
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 13.9394 |
| f_angle_d | 1.2346 |
| f_chiral_restr | 0.0763 |
| f_bond_d | 0.0133 |
| f_plane_restr | 0.0079 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 869 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 97 |
| Heterogen Atoms | 1 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| PHENIX | refinement |
| XDS | data reduction |
| Aimless | data scaling |
| PHASER | phasing |
