1Y2C
Catalytic Domain Of Human Phosphodiesterase 4D In Complex With 3,5-dimethyl-1-phenyl-1H-pyrazole-4-carboxylic acid ethyl ester
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 288 | PEG3350, ethylene glycol, isopropanol, glycerol and DTT, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 288K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.44 | 49.65 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 60.688 | α = 90 |
b = 78.966 | β = 90 |
c = 163.51 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 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 | 93 | CCD | ADSC QUANTUM 210 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 8.3.1 | 1.1 | ALS | 8.3.1 |
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 | 1.67 | 81.65 | 99.51 | 0.119 | 3.6 | 3.7 | 86926 | 86926 |
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 | 1.67 | 1.713 | 99.9 | 0.447 | 1.6 | 3.7 | 6397 |
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 (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 1.67 | 81.65 | 86926 | 86926 | 4579 | 99.51 | 0.17733 | 0.17733 | 0.17666 | 0.19017 | RANDOM | 16.465 |
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] | |
-0.72 | 0.44 | 0.28 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_1_deg | 2.745 |
r_scangle_it | 2.478 |
r_scbond_it | 1.469 |
r_angle_refined_deg | 1.096 |
r_angle_other_deg | 0.876 |
r_mcangle_it | 0.82 |
r_mcbond_it | 0.419 |
r_symmetry_vdw_other | 0.308 |
r_nbd_other | 0.226 |
r_nbd_refined | 0.21 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5276 |
Nucleic Acid Atoms | |
Solvent Atoms | 351 |
Heterogen Atoms | 132 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
Blu-Ice | data collection |
ELVES | data scaling |
EPMR | phasing |