5ETQ
S. aureus 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase complexed with AMPCPP and inhibitor at 1.96 angstrom resolution
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4CWB |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 281 | PROTEIN 6.9 MG/ML, 1 MM AMPCPP, 1 MM INHIBITOR, 0.202 M MAGNESIUM CHLORIDE, 0.1 M TRIS CHLORIDE, 20%w/v PEG8000, 50 MM SODIUM THIOCYANATE |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.25 | 45.36 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 47.63 | ¦Á = 90 |
b = 68.2 | ¦Â = 106.05 |
c = 52.82 | ¦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 | 2015-02-07 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | AUSTRALIAN SYNCHROTRON BEAMLINE MX2 | 0.9707 | 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 | 1.96 | 68.2 | 100 | 0.117 | 9.1 | 7 | 23517 |
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 | 1.96 | 2.01 | 99.8 | 0.497 | 3.2 | 6.6 |
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 | 4CWB | 1.96 | 50.76 | 22352 | 1146 | 99.94 | 0.18384 | 0.18219 | 0.21566 | RANDOM | 12.433 |
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] | |
-0.19 | -0.92 | 2.16 | -1.23 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.713 |
r_dihedral_angle_4_deg | 12.936 |
r_dihedral_angle_3_deg | 11.845 |
r_dihedral_angle_1_deg | 6.36 |
r_long_range_B_refined | 6.351 |
r_long_range_B_other | 6.351 |
r_scangle_other | 5.092 |
r_angle_other_deg | 3.613 |
r_scbond_it | 3.499 |
r_scbond_other | 3.497 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2508 |
Nucleic Acid Atoms | |
Solvent Atoms | 136 |
Heterogen Atoms | 111 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
Aimless | data scaling |
XDS | data reduction |
MOLREP | phasing |
Coot | model building |