4CYU
Staphylococcus aureus 7,8-Dihydro-6-hydroxymethylpterin- pyrophosphokinase in complex with AMPCPP
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4AD6 | PDB ENTRY 4AD6 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8 | 281 | PROTEIN 6.9 MG/ML 1 MM AMPCPP, 2 MM MAGNESIUM CHLORIDE, MAGNESIUM ACETATE 0.119 M, PEG8000 12.6% W/V, TRIS CHLORIDE 0.12 M, SITTING DROP, 281 K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.39 | 48.62 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 62.002 | ¦Á = 90 |
b = 94.263 | ¦Â = 112.44 |
c = 62.989 | ¦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 CCD | 2013-12-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | AUSTRALIAN SYNCHROTRON BEAMLINE MX2 | 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 | 2.7 | 45.53 | 100 | 0.14 | 9.4 | 7.5 | 18506 |
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 | 2.7 | 2.83 | 100 | 0.9 | 2.1 | 7.3 |
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 | PDB ENTRY 4AD6 | 2.7 | 45.53 | 17651 | 838 | 99.96 | 0.19433 | 0.19217 | 0.24223 | RANDOM | 54.203 |
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] | |
0.16 | 2.65 | 0.06 | -0.98 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.791 |
r_dihedral_angle_4_deg | 16.655 |
r_dihedral_angle_3_deg | 14.635 |
r_dihedral_angle_1_deg | 6.304 |
r_angle_other_deg | 3.437 |
r_angle_refined_deg | 1.493 |
r_chiral_restr | 0.071 |
r_bond_refined_d | 0.01 |
r_gen_planes_refined | 0.005 |
r_gen_planes_other | 0.005 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4999 |
Nucleic Acid Atoms | |
Solvent Atoms | 13 |
Heterogen Atoms | 148 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
SCALA | data scaling |
PHASER | phasing |