5ETM
E. coli 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase complexed with AMPCPP and inhibitor at 1.46 angstrom resolution
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5ETK |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.55 | 293 | Protein 6.6 mg/mL, 1 mM AMPCPP, 1 mM inhibitor, 2 mM Magnesium Chloride, 27.5 %w/v PEG4000, 0.1 M sodium HEPES, 0.196 M Calcium Chloride |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.95 | 36.95 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 35.763 | ¦Á = 90 |
b = 57.631 | ¦Â = 115.49 |
c = 38.407 | ¦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 | ADSC QUANTUM 315r | 2015-09-26 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | AUSTRALIAN SYNCHROTRON BEAMLINE MX2 | 0.9537 | Australian Synchrotron | MX2 |
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 | 1.46 | 34.67 | 99.8 | 0.097 | 11.6 | 7.1 | 24472 |
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 | 1.46 | 1.48 | 99.9 | 0.662 | 2.7 | 6.5 |
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 | 5ETK | 1.46 | 34.67 | 23060 | 1391 | 99.76 | 0.2063 | 0.20441 | 0.23939 | RANDOM | 12.946 |
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] | |
0.48 | -0.42 | -0.03 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.376 |
r_dihedral_angle_4_deg | 17.167 |
r_dihedral_angle_3_deg | 11.552 |
r_dihedral_angle_1_deg | 6.733 |
r_long_range_B_refined | 4.291 |
r_long_range_B_other | 4.245 |
r_angle_other_deg | 3.558 |
r_scangle_other | 2.781 |
r_angle_refined_deg | 2.206 |
r_mcangle_it | 2.046 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1275 |
Nucleic Acid Atoms | |
Solvent Atoms | 88 |
Heterogen Atoms | 57 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
Coot | model building |
Aimless | data scaling |
XDS | data reduction |
MOLREP | phasing |