6JBA
Crystal structure of ABC transporter alpha-glycoside-binding mutant protein W287A in complex with palatinose
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | MICROBATCH | 6.4 | 277 | 0.04 M Citric Acid, 0.06 M Bis-Tris Propane, 16% PEG 3350 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.83 | 56.59 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 84.1 | α = 90 |
b = 84.1 | β = 90 |
c = 146.02 | γ = 90 |
Symmetry | |
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Space Group | P 41 21 2 |
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 | IMAGE PLATE | RIGAKU RAXIS IV++ | VariMax HF | 2018-04-22 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU MICROMAX-007 HF | 1.5418 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | 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 | 2 | 72.88 | 100 | 0.14 | 0.158 | 0.073 | 0.99 | 10.4 | 8.5 | 36237 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 2 | 8.94 | 100 | 0.574 | 0.653 | 0.308 | 0.917 | 3.4 | 8.4 |
Refinement
Statistics | |||||||||||||||||||
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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 | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 6J9W | 2 | 72.88 | 34304 | 1849 | 99.97 | 0.1525 | 0.1506 | 0.1863 | RANDOM | 22.99 |
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] | |
0.96 | 0.96 | -1.92 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.154 |
r_dihedral_angle_4_deg | 15.827 |
r_dihedral_angle_3_deg | 13.83 |
r_dihedral_angle_1_deg | 5.887 |
r_angle_refined_deg | 1.787 |
r_angle_other_deg | 0.903 |
r_chiral_restr | 0.104 |
r_bond_refined_d | 0.017 |
r_gen_planes_refined | 0.01 |
r_bond_other_d | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3218 |
Nucleic Acid Atoms | |
Solvent Atoms | 448 |
Heterogen Atoms | 48 |
Software
Software | |
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Software Name | Purpose |
HKL-3000 | data collection |
iMOSFLM | data reduction |
Aimless | data scaling |
PHASER | phasing |
REFMAC | refinement |
Coot | model building |
PDB_EXTRACT | data extraction |