4RXT
Crystal structure of carbohydrate transporter solute binding protein Arad_9553 from Agrobacterium Radiobacter, Target EFI-511541, in complex with D-arabinose
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 294 | PROTEIN (10 MM HEPES PH 7.5, 5 MM DTT, 10 MM D-ARABINOSE); RESERVOIR: 0.1 M TRIS-HCL, PH 8.5, 2.5 M AMMONIUM SULFATE; CRYOPROTECTION: RESERVOIR SOLUTION; VAPOR DIFFUSION, SITTING DROP, temperature 294K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.04 | 39.59 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( ? ) | Angle ( ? ) |
| a = 59.873 | ¦Á = 90 |
| b = 36.244 | ¦Â = 110.01 |
| c = 62.1 | ¦Ã = 90 |
| Symmetry | |
|---|---|
| Space Group | P 1 21 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 | RAYONIX MX225HE | MIRRORS | 2014-12-05 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | APS BEAMLINE 31-ID | APS | 31-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 | 1.35 | 50 | 99.1 | 0.108 | 11.3 | 4.4 | 55996 | -3 | |||||||||||
| 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 | 1.35 | 1.37 | 99.2 | 0.89 | 2.4 | 4.2 | |||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | 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 | SAD | THROUGHOUT | 1.35 | 50 | 53008 | 1633 | 98.63 | 0.15747 | 0.15597 | 0.20547 | RANDOM | 20.363 | |||||||
| 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] | |
| -1.32 | -1.07 | 4.53 | -1.92 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 38.452 |
| r_sphericity_free | 38.31 |
| r_dihedral_angle_4_deg | 22.131 |
| r_sphericity_bonded | 16.011 |
| r_dihedral_angle_3_deg | 13.694 |
| r_scbond_other | 7.127 |
| r_scbond_it | 7.125 |
| r_scangle_other | 6.634 |
| r_long_range_B_refined | 6.564 |
| r_long_range_B_other | 6.563 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 2149 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 333 |
| Heterogen Atoms | 10 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| SHELX | model building |
| ARP/wARP | model building |
| REFMAC | refinement |
| HKL-3000 | data reduction |
| HKL-3000 | data scaling |
| SHELX | phasing |
