4RY0
Crystal structure of ribose transporter solute binding protein RHE_PF00037 from Rhizobium etli CFN 42, TARGET EFI-511357, in complex with D-ribose
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | 8.5 | PROTEIN (10 MM HEPES PH 7.5, 5 MM DTT, 10 MM D-RIBOSE); RESERVOIR: 0.2 M CALCIUM CHLORIDE, 0.1 M TRIS-HCL, PH 8.5, 20% (w/v) PEG 4000; CRYOPROTECTION: RESERVOIR SOLUTION PLUS 20% D-GLUCOSE SOLUTION; VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K | ||
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.36 | 47.82 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( ? ) | Angle ( ? ) |
| a = 93.11 | ¦Á = 90 |
| b = 36.766 | ¦Â = 117.91 |
| c = 95.48 | ¦Ã = 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 | 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 | 1.4 | 50 | 98 | 0.103 | 22.2 | 7.5 | 57304 | -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 | 1.4 | 1.42 | 96.6 | 0.8 | 2.57 | 7.5 | |||||||||||||
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 | 1.4 | 24 | 53653 | 1724 | 97.66 | 0.1446 | 0.14341 | 0.18106 | RANDOM | 19.268 | |||||||
| 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] | |
| -0.65 | -1.08 | 3.84 | -1.31 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 39.674 |
| r_sphericity_free | 30.549 |
| r_sphericity_bonded | 15.754 |
| r_dihedral_angle_3_deg | 14.736 |
| r_dihedral_angle_4_deg | 10.484 |
| r_scbond_it | 7.959 |
| r_scbond_other | 7.959 |
| r_scangle_other | 6.98 |
| r_long_range_B_refined | 6.434 |
| r_long_range_B_other | 6.34 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 2120 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 261 |
| Heterogen Atoms | 12 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| SHELX | model building |
| ARP/wARP | model building |
| REFMAC | refinement |
| HKL-3000 | data reduction |
| HKL-3000 | data scaling |
| SHELX | phasing |
