8I6D
Crystal structure of Mycobacterium tuberculosis Uracil-DNA glycosylase in complex with 5-Hydroxy-2,4(1H,3H)-pyrimidinedione, Form VI
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4WS4 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | MICROBATCH | 293 | 0.1 M Tris pH 6.5, 1.4 M Sodium citrate, 15% PEG (w/v) 3350, 2% Benzamidine hydrochloride |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.02 | 39.01 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 45.98 | ¦Á = 90 |
b = 77.99 | ¦Â = 102.02 |
c = 59.37 | ¦Ã = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
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 | MAR scanner 345 mm plate | 2020-08-20 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | BRUKER AXS MICROSTAR | 1.5418 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 2.4 | 25.61 | 96.28 | 0.1249 | 0.973 | 5.55 | 2 | 15539 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.4 | 2.486 | 0.391 | 0.667 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 4WS4 | 2.4 | 25.61 | 14784 | 755 | 96.29 | 0.2032 | 0.19986 | 0.26973 | RANDOM | 17.162 |
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] | |
0.89 | -0.91 | -1.21 | 0.65 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.584 |
r_dihedral_angle_4_deg | 16.025 |
r_dihedral_angle_3_deg | 15.698 |
r_dihedral_angle_1_deg | 7.336 |
r_long_range_B_refined | 3.516 |
r_long_range_B_other | 3.509 |
r_mcangle_it | 1.675 |
r_mcangle_other | 1.675 |
r_scangle_other | 1.503 |
r_angle_refined_deg | 1.476 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3342 |
Nucleic Acid Atoms | |
Solvent Atoms | 141 |
Heterogen Atoms | 38 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
iMOSFLM | data reduction |
SCALA | data scaling |
PHASER | phasing |