6EI3
Crystal structure of auto inhibited POT family peptide transporter
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4APS |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | LIPIDIC CUBIC PHASE | 8.5 | 292 | 100 mM TrisHCl, 120 mM ammonium tartrate, 20 %(v/v) PEG 400, pH 8.5 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.78 | 55.7 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 138.06 | α = 90 |
b = 65.23 | β = 96.84 |
c = 70.34 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 1 |
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 | 277 | PIXEL | DECTRIS PILATUS3 S 6M | 2013-09-07 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I24 | 0.96859 | Diamond | I24 |
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 | 2.1 | 24.65 | 99.9 | 0.097 | 0.103 | 0.035 | 0.999 | 15.2 | 8.2 | 36377 | 36.14 |
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 | 2.1 | 2.15 | 99.9 | 0.686 | 0.774 | 0.354 | 0.782 | 4.6 |
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 | 4APS | 2.1 | 24.65 | 36377 | 1816 | 99.95 | 0.1809 | 0.1792 | 0.2135 | RANDOM | 45.29 |
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] | |
-2.9554 | 1.2052 | 3.4976 | -0.5422 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
t_other_torsion | 18.04 |
t_omega_torsion | 2.85 |
t_angle_deg | 0.94 |
t_bond_d | 0.01 |
t_dihedral_angle_d | |
t_trig_c_planes | |
t_gen_planes | |
t_it | |
t_nbd | |
t_improper_torsion |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3986 |
Nucleic Acid Atoms | |
Solvent Atoms | 288 |
Heterogen Atoms | 346 |
Software
Software | |
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Software Name | Purpose |
Aimless | data scaling |
BUSTER | refinement |
PDB_EXTRACT | data extraction |
XDS | data reduction |
PHASER | phasing |