3RL5
Rat metallophosphodiesterase MPPED2 H67R Mutant
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.2 | 293 | Ammonium nitrate, PEG 3350, CaCl2, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.36 | 47.82 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 98.622 | α = 90 |
b = 69.848 | β = 103.52 |
c = 47.182 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 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 | MAR CCD 165 mm | monochromators, mirrors | 2009-01-22 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ELETTRA BEAMLINE 5.2R | 0.99996 | ELETTRA | 5.2R |
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 | 1.26 | 50 | 99.9 | 0.059 | 16.9 | 4.1 | 84002 | 83943 | -3 | 11.242 |
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 | 1.26 | 1.29 | 99.2 | 0.251 | 3.9 | 5512 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | 1.26 | 20.75 | 84002 | 83935 | 8430 | 99.92 | 0.1542 | 0.1519 | 0.1744 | RANDOM | 16.8614 |
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] | |
0.27 | -0.39 | -0.1 | -0.35 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.423 |
r_dihedral_angle_4_deg | 14.253 |
r_dihedral_angle_3_deg | 10.556 |
r_dihedral_angle_1_deg | 6.279 |
r_sphericity_free | 5.16 |
r_sphericity_bonded | 4.09 |
r_scangle_it | 3.475 |
r_scbond_it | 3.124 |
r_rigid_bond_restr | 2.939 |
r_mcangle_it | 2.045 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2250 |
Nucleic Acid Atoms | |
Solvent Atoms | 285 |
Heterogen Atoms | 10 |
Software
Software | |
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Software Name | Purpose |
SCALEPACK | data scaling |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
HKL-2000 | data collection |
DENZO | data reduction |