7CWF
Crystal structure of PDE8A catalytic domain in complex with 2c
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3ECM |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 277 | 100mM Cacodylate Sodium pH 6.5, 15% Isopropanol, 30% Ethylene Glycol, 11% PEG3350 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.35 | 62.21 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 76.114 | α = 90 |
b = 131.874 | β = 90 |
c = 101.398 | γ = 90 |
Symmetry | |
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Space Group | C 2 2 21 |
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 | OXFORD ONYX CCD | 2020-07-30 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SEALED TUBE | OXFORD DIFFRACTION NOVA | 1.5406 |
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 | 2.8 | 23.66 | 99.5 | 0.068 | 22.16 | 5 | 12282 |
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 | 2.8 | 2.9 | 100 | 0.256 | 5.52 | 5.2 |
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 | 3ECM | 2.8 | 23.66 | 12244 | 622 | 99.56 | 0.25851 | 0.25675 | 0.29258 | RANDOM | 47.217 |
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] | |
-3.91 | -1.77 | 5.68 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.804 |
r_dihedral_angle_3_deg | 11.184 |
r_dihedral_angle_4_deg | 10.77 |
r_dihedral_angle_1_deg | 4.392 |
r_long_range_B_refined | 2.855 |
r_long_range_B_other | 2.836 |
r_mcangle_it | 1.272 |
r_mcangle_other | 1.271 |
r_angle_refined_deg | 0.921 |
r_angle_other_deg | 0.844 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2727 |
Nucleic Acid Atoms | |
Solvent Atoms | 52 |
Heterogen Atoms | 25 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
CrysalisPro | data reduction |
CrysalisPro | data scaling |
MOLREP | phasing |