4S2U
Crystal structure of the Phosphorybosylpyrophosphate synthetase from E. Coli
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | COUNTER-DIFFUSION | 7.5 | 293 | 0.1 M TRIS-buffer pH 8.5, 0.3M NaCl, 2 mM MgCl2, 04% NaN3, 15% Ammonium Sulphate, COUNTER DIFFUSION, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.89 | 57.49 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 104.599 | α = 90 |
b = 104.599 | β = 90 |
c = 125.78 | γ = 120 |
Symmetry | |
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Space Group | P 63 2 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | PIXEL | PSI PILATUS 6M | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SPRING-8 BEAMLINE BL41XU | 0.8 | SPring-8 | BL41XU |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 2.71 | 30 | 95.67 | 0.09 | 7.96 | 12.22 | 10949 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | 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 | 2.71 | 29.36 | 10425 | 521 | 94.43 | 0.25237 | 0.24974 | 0.30433 | RANDOM | 52.14 |
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] | |
0.54 | 0.54 | 0.54 | -1.76 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.447 |
r_dihedral_angle_3_deg | 18.372 |
r_dihedral_angle_4_deg | 13.366 |
r_dihedral_angle_1_deg | 7.264 |
r_angle_refined_deg | 1.519 |
r_angle_other_deg | 0.834 |
r_chiral_restr | 0.081 |
r_bond_refined_d | 0.008 |
r_gen_planes_refined | 0.005 |
r_bond_other_d | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2339 |
Nucleic Acid Atoms | |
Solvent Atoms | 11 |
Heterogen Atoms | 1 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data collection |
PHASER | phasing |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |