6JB0
Crystal structure of ABC transporter alpha-glycoside-binding mutant protein W287A in complex with trehalose
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
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 |
2.88 | 57.32 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 84.76 | α = 90 |
b = 84.76 | β = 90 |
c = 146.21 | γ = 90 |
Symmetry | |
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Space Group | P 41 21 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2018-04-21 | 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 | 1.63 | 73.33 | 96.9 | 0.061 | 0.066 | 0.025 | 0.999 | 24.4 | 12.3 | 65184 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.63 | 8.92 | 91.5 | 0.381 | 0.414 | 0.16 | 0.942 | 5.7 | 11.9 |
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 | 1.63 | 73.33 | 61940 | 3155 | 96.82 | 0.1355 | 0.1342 | 0.1602 | RANDOM | 16.13 |
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] | |
0.21 | 0.21 | -0.41 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.311 |
r_dihedral_angle_4_deg | 16.946 |
r_dihedral_angle_3_deg | 12.601 |
r_dihedral_angle_1_deg | 5.722 |
r_angle_refined_deg | 1.947 |
r_angle_other_deg | 0.933 |
r_chiral_restr | 0.123 |
r_bond_refined_d | 0.02 |
r_gen_planes_refined | 0.012 |
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 | 620 |
Heterogen Atoms | 55 |
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 |