5XZ7
Crystal Structure of Phosphofructokinase from Staphylococcus aureus in complex with adenylylimidodiphosphate, the ATP analogue
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 283 | 15% PEG4000, 0.1M MES PH 6.0 , 0.15M(NH4)2SO4 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.56 | 51.95 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 73.56 | α = 90 |
b = 80.2 | β = 90 |
c = 121.3 | γ = 90 |
Symmetry | |
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Space Group | I 2 2 2 |
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 | 2013-12-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRF BEAMLINE BL17U1 | 0.9793 | SSRF | BL17U1 |
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 | 1.6 | 66.9 | 100 | 0.107 | 11.6 | 6.2 | 47521 | 12.6 |
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 | 1.6 | 1.69 | 100 | 0.417 | 4.3 | 5.3 |
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 | 5XOE | 1.6 | 66.9 | 45110 | 2404 | 99.93 | 0.15514 | 0.15389 | 0.17881 | RANDOM | 15.544 |
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] | |
0.56 | -0.23 | -0.33 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.488 |
r_dihedral_angle_4_deg | 14.811 |
r_dihedral_angle_3_deg | 12.535 |
r_long_range_B_refined | 6.053 |
r_long_range_B_other | 6.053 |
r_dihedral_angle_1_deg | 5.028 |
r_scangle_other | 4.496 |
r_scbond_it | 3.07 |
r_scbond_other | 3.07 |
r_mcangle_other | 2.341 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2446 |
Nucleic Acid Atoms | |
Solvent Atoms | 284 |
Heterogen Atoms | 59 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
iMOSFLM | data reduction |
SCALA | data scaling |
PHASER | phasing |