8RHY
Crystal Structure of Trypanosoma brucei PTR1 in complex with the cofactor and inhibitor P34
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 6TBX |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5 | 297 | 1.6-2.5 M sodium acetate and 0.1 M sodium citrate, pH 5 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.15 | 42.77 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 74.365 | ¦Á = 90 |
b = 99.091 | ¦Â = 115.86 |
c = 84.447 | ¦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 PILATUS 6M | 2023-03-20 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I24 | 0.99989 | 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 | 1.86 | 75.84 | 98 | 0.111 | 0.138 | 0.08 | 0.992 | 6.9 | 4.8 | 89898 | 2 | 23.7 |
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 | 1.86 | 1.89 | 96.6 | 0.755 | 0.95 | 0.569 | 0.756 | 2 | 4.8 |
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 | MOLECULAR REPLACEMENT | THROUGHOUT | 1.86 | 75.84 | 82814 | 4713 | 94.71 | 0.18477 | 0.18264 | 0.22302 | RANDOM | 11.253 |
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] | |
-0.01 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_3_deg | 13.496 |
r_dihedral_angle_1_deg | 6.392 |
r_dihedral_angle_2_deg | 6.098 |
r_long_range_B_refined | 4.331 |
r_mcangle_it | 1.96 |
r_angle_refined_deg | 1.863 |
r_scbond_it | 1.48 |
r_mcbond_it | 1.174 |
r_chiral_restr | 0.12 |
r_bond_refined_d | 0.01 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7361 |
Nucleic Acid Atoms | |
Solvent Atoms | 698 |
Heterogen Atoms | 252 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
Aimless | data scaling |
MOLREP | phasing |