4EF6
Crystal Structure of Mycobacterium tuberculosis Pantothenate synthetase in complex with fragment 1
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3COV |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8 | 293 | 12-14% PEG 3000, 150 mM Li2SO4, 100 mM Imidazole, 2% Ethanol, 5% Glycerol, 20 mM MgCl2, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.18 | 43.62 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 48.12 | ¦Á = 90 |
b = 70.7 | ¦Â = 99.48 |
c = 82.11 | ¦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 | CCD | MARMOSAIC 225 mm CCD | 2008-06-30 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X06DA | 0.97 | SLS | X06DA |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 1.94 | 38.29 | 99.5 | 0.115 | 12 | 4.2 | 170443 | 40119 | 20.55 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.94 | 2.04 | 96.5 | 0.668 | 1.7 | 3.1 | 17682 |
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 | 3COV | 1.94 | 38.29 | 38082 | 2009 | 99.41 | 0.16671 | 0.16397 | 0.21809 | RANDOM | 23.298 |
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] | |
0.68 | -0.44 | 1.02 | -1.85 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.912 |
r_dihedral_angle_3_deg | 15.24 |
r_dihedral_angle_4_deg | 14.593 |
r_dihedral_angle_1_deg | 6.572 |
r_scangle_it | 4.658 |
r_scbond_it | 3.036 |
r_angle_refined_deg | 1.875 |
r_mcangle_it | 1.807 |
r_mcbond_it | 1.1 |
r_chiral_restr | 0.126 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4161 |
Nucleic Acid Atoms | |
Solvent Atoms | 489 |
Heterogen Atoms | 85 |
Software
Software | |
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Software Name | Purpose |
PHASER | phasing |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |