4RY9
Crystal structure of carbohydrate transporter solute binding protein VEIS_2079 from Verminephrobacter eiseniae EF01-2, TARGET EFI-511009, a complex with D-TALITOL
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 7.5 | PROTEIN (10 MM HEPES PH 7.5, 5 MM DTT, 10 MM D-TALITOL) RESERVOIR: 0.2 M POTASSIUM SULFATE, 25% PEG3350 CRYOPROTECTION: RESERVOIR SOLUTION PLUS 25% (V/V) GLYCEROL VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.22 | 44.65 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 68.65 | α = 90 |
b = 68.635 | β = 90 |
c = 120.376 | γ = 90 |
Symmetry | |
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Space Group | P 2 2 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
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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 | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 31-ID | APS | 31-ID |
Data Collection
Overall | |||||||||||||||||||
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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 | 97.5 | 0.095 | 33.9 | 15 | 113208 | -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 | 95.4 | 0.98 | 2.8 | 13.9 |
Refinement
Statistics | |||||||||||||||||||
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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 | 25 | 106509 | 3259 | 97.58 | 0.12403 | 0.12322 | 0.1509 | RANDOM | 18.091 |
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] | |
0.39 | 0.48 | -0.87 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 38.603 |
r_sphericity_free | 24.359 |
r_dihedral_angle_3_deg | 12.469 |
r_sphericity_bonded | 11.595 |
r_dihedral_angle_4_deg | 11.41 |
r_scbond_other | 7.199 |
r_scbond_it | 7.193 |
r_scangle_other | 6.016 |
r_dihedral_angle_1_deg | 5.789 |
r_long_range_B_refined | 4.754 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4394 |
Nucleic Acid Atoms | |
Solvent Atoms | 537 |
Heterogen Atoms | 112 |
Software
Software | |
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Software Name | Purpose |
SHELX | model building |
ARP/wARP | model building |
REFMAC | refinement |
HKL-3000 | data reduction |
HKL-3000 | data scaling |
SHELX | phasing |