1L4U
CRYSTAL STRUCTURE OF SHIKIMATE KINASE FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH MGADP AND PT(II) AT 1.8 ANGSTROM RESOLUTION
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 288 | PEG 4000, magnesium choloride, sodium chloride, ADENOSINE-5'-DIPHOSPHATE, SHIKIMIC ACID, NAHEPES, PLATINUM POTASSIUM CHLORIDE, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.9 | 57.63 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 63.83 | α = 90 |
b = 63.83 | β = 90 |
c = 91.92 | γ = 120 |
Symmetry | |
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Space Group | P 32 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 | CCD | ADSC QUANTUM 4 | MIRROR | 1999-08-03 | M | MAD | |||||
2 | 1 | |||||||||||||
3 | 1 | |||||||||||||
4 | 1 |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X9B | 1.07223,1.07186,1.06268,1.08121 | NSLS | X9B |
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 | 1.8 | 19.02 | 99.7 | 0.104 | 0.08 | 10.134 | 6.64 | 20677 | 20594 | -3 | 23.2 |
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 | 1.8 | 1.86 | 99.8 | 0.176 | 0.165 | 4.34 | 5.86 | 2035 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MAD | THROUGHOUT | 1.8 | 20 | 20594 | 20594 | 999 | 99.7 | 0.221 | 0.249 | RANDOM | 30.9 |
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] | |
2.67 | -0.32 | 2.67 | -5.34 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 20.1 |
c_scangle_it | 2.97 |
c_scbond_it | 2.01 |
c_mcangle_it | 1.99 |
c_mcbond_it | 1.27 |
c_angle_deg | 1.1 |
c_improper_angle_d | 0.75 |
c_bond_d | 0.005 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1226 |
Nucleic Acid Atoms | |
Solvent Atoms | 194 |
Heterogen Atoms | 50 |
Software
Software | |
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Software Name | Purpose |
PHASES | phasing |
CNS | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |