6GEX
Trypanosoma brucei PTR1 in complex with inhibitor 2h (F246)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5JDC |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5 | 297 | 2-2.5 M sodium acetate, 0.1 M sodium citrate, pH5 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.1 | 41.4 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 74.881 | ¦Á = 90 |
b = 90.214 | ¦Â = 115.76 |
c = 83.154 | ¦Ã = 90 |
Symmetry | |
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Space Group | P 1 21 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 | 100 | PIXEL | DECTRIS PILATUS3 X 2M | 2017-11-23 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID23-2 | 0.87313 | ESRF | ID23-2 |
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 | 1.78 | 90.21 | 99.2 | 0.08 | 0.096 | 0.053 | 0.997 | 9.8 | 3.3 | 94517 | 2 | 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 | 1.78 | 1.88 | 98.8 | 0.647 | 0.774 | 0.421 | 0.715 | 2 | 3.3 |
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 | 5JDC | 1.78 | 74.89 | 89589 | 4859 | 99.08 | 0.16827 | 0.16612 | 0.20659 | RANDOM | 18.073 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.06 |
r_dihedral_angle_4_deg | 20.226 |
r_dihedral_angle_3_deg | 13.44 |
r_dihedral_angle_1_deg | 6.299 |
r_long_range_B_refined | 5.507 |
r_mcangle_it | 2.641 |
r_scbond_it | 2.449 |
r_angle_refined_deg | 1.985 |
r_mcbond_it | 1.797 |
r_chiral_restr | 0.125 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7288 |
Nucleic Acid Atoms | |
Solvent Atoms | 661 |
Heterogen Atoms | 276 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
SCALA | data scaling |
MOLREP | phasing |