1K9Y
The PAPase Hal2p complexed with magnesium ions and reaction products: AMP and inorganic phosphate
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 293 | 30 % PEG5000 MME, 0.1 M sodium acetate, 5 mM beta-mercaptoethanol, 0.1 M MES (Crystals were soaked in mother liquor containing 1 M magnesium chloride for 1 hour), pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.11 | 41.66 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 54.693 | α = 90 |
b = 45.075 | β = 110.96 |
c = 71.794 | γ = 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 | IMAGE PLATE | RIGAKU RAXIS | 1999-08-08 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU | 1.5418 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.9 | 67.42 | 99.5 | 25897 | 25897 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1.9 | 1.949 | 99.5 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | 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 1QGX | 1.9 | 67.42 | 25847 | 25847 | 1306 | 99.43 | 0.15845 | 0.1559 | 0.20348 | RANDOM | 19.369 |
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] | |
-1.74 | -0.42 | 1.47 | -0.03 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_3_deg | 17.566 |
r_dihedral_angle_1_deg | 6.346 |
r_scangle_it | 5.933 |
r_scbond_it | 3.982 |
r_mcangle_it | 2.656 |
r_angle_refined_deg | 1.739 |
r_mcbond_it | 1.711 |
r_angle_other_deg | 0.83 |
r_symmetry_hbond_refined | 0.349 |
r_symmetry_vdw_refined | 0.247 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2727 |
Nucleic Acid Atoms | |
Solvent Atoms | 235 |
Heterogen Atoms | 35 |
Software
Software | |
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Software Name | Purpose |
MOSFLM | data reduction |
SCALA | data scaling |
REFMAC | refinement |
CCP4 | data scaling |