4BQS
Crystal structure of Mycobacterium tuberculosis shikimate kinase in complex with ADP and a shikimic acid derivative.
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2G1K | PDB ENTRY 2G1K |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.8 | 291 | VAPOR DIFUSION, SITTING DROP, 20% (W/V) PEG 3350, 500 MM LICL AND 100 MM TRIS.HCL PH 7.8, ATP, SHIKIMIC ACID DERIVATIVE, TEMPERATURE 291 K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.07 | 40.63 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 40.653 | ¦Á = 90 |
b = 60.959 | ¦Â = 95.44 |
c = 89.976 | ¦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 | MIRRORS | 2013-05-03 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I02 | Diamond | I02 |
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 | 2.15 | 28.85 | 95.6 | 0.08 | 11.1 | 3.3 | 22876 | 2 | 21 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.15 | 2.27 | 79.4 | 0.34 | 3.5 | 3 |
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 | PDB ENTRY 2G1K | 2.15 | 28.87 | 21698 | 1165 | 95.27 | 0.17554 | 0.1723 | 0.23506 | RANDOM | 30.371 |
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] | |
1.07 | 2.91 | -0.79 | -0.55 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 30.213 |
r_dihedral_angle_4_deg | 20.378 |
r_dihedral_angle_3_deg | 15.562 |
r_scangle_it | 6.953 |
r_dihedral_angle_1_deg | 5.853 |
r_scbond_it | 5.812 |
r_mcangle_it | 3.777 |
r_mcbond_it | 2.467 |
r_angle_refined_deg | 1.747 |
r_angle_other_deg | 0.856 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3774 |
Nucleic Acid Atoms | |
Solvent Atoms | 141 |
Heterogen Atoms | 126 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
SCALA | data scaling |
MOLREP | phasing |