2GET
Pantothenate kinase from Mycobacterium tuberculosis (MtPanK) in complex with a coenzyme A derivative, Form-I (LT)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1ESM | PDB ID 1ESM |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 293 | 10-15%(w/v) PEG8000, 0.05M NaCl, 0.05-0.1M NaOAc in 0.1M Na-Cacodylate buffer of pH 6.5, 0.001M Beta-mercaptoethanol was present in the protein buffer, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.7 | 53.3 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 76.973 | ¦Á = 90 |
b = 76.973 | ¦Â = 90 |
c = 113.647 | ¦Ã = 120 |
Symmetry | |
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Space Group | P 31 2 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 | IMAGE PLATE | MARRESEARCH | 2005-01-03 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU ULTRAX 18 | 1.5418 |
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 | 2.35 | 28.75 | 99.6 | 0.059 | 22.7 | 9.9 | 16654 | -3 | 53.3 |
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 | 2.35 | 2.43 | 99.9 | 0.562 | 3.7 | 6.4 | 1630 |
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 (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ID 1ESM | 2.35 | 28.75 | 16654 | 817 | 99.4 | 0.227 | 0.227 | 0.22 | 0.27 | 0.26 | RANDOM | 64.3 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
-0.55 | 3.23 | 2.4 | -1.85 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 23.7 |
c_scangle_it | 2.85 |
c_mcangle_it | 2.54 |
c_scbond_it | 1.95 |
c_mcbond_it | 1.51 |
c_angle_deg | 1.3 |
c_improper_angle_d | 0.9 |
c_bond_d | 0.007 |
c_bond_d_na | |
c_bond_d_prot |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2483 |
Nucleic Acid Atoms | |
Solvent Atoms | 175 |
Heterogen Atoms | 64 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
CNS | refinement |
MAR345 | data collection |
CCP4 | data scaling |
AMoRE | phasing |