3CE6
Crystal structure of Mycobacterium tuberculosis S-adenosyl-L-homocysteine hydrolase in ternary complex with NAD and adenosine
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1LI4 | PDB ENTRY 1LI4 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 8 | 291.5 | 20% PEG 1000, 200 mM Imidazole pH 8.0, 100 mM Calcium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 291.5K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.51 | 51.01 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 97.04 | ¦Á = 90 |
b = 112.133 | ¦Â = 92.41 |
c = 100.234 | ¦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 | 120 | CCD | ADSC QUANTUM 315 | MIRRORS | 2005-03-04 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 19-ID | APS | 19-ID |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym I (Observed) | 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 | 1.5 | 100 | 94.9 | 0.0487 | 0.0487 | 13.1 | 308888 | 2 | 17 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.5 | 1.54 | 73.4 | 0.6821 | 0.6821 | 1.48 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | 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 | PDB ENTRY 1LI4 | 1.6 | 30 | 308888 | 273464 | 13795 | 97.1 | 0.202 | 0.2 | 0.238 | RANDOM | 18.37 |
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] | |
1.52 | 0.31 | -1.09 | -0.41 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.095 |
r_dihedral_angle_4_deg | 19.471 |
r_dihedral_angle_3_deg | 13.642 |
r_scangle_it | 7.496 |
r_dihedral_angle_1_deg | 6.531 |
r_scbond_it | 5.82 |
r_mcangle_it | 3.811 |
r_mcbond_it | 3.175 |
r_angle_refined_deg | 2.394 |
r_nbtor_refined | 0.311 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 14996 |
Nucleic Acid Atoms | |
Solvent Atoms | 1736 |
Heterogen Atoms | 252 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
AMoRE | phasing |