5WH5
Crystal structure of the PDE4D2 catalytic domain in complex with inhibitor (R)-Zl-n-91
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | EVAPORATION | 7.5 | 277 | The ~10mg/ml PDE4D2 (86-413) was stored in a buffer of 20 mM Tris.base, pH 7.5, 50 mM NaCl, 1 mM 2-mercaptoethanol, 1 mM EDTA and mixed with 2 mM (R)- or (S)-5. They were crystallized at 4C by hanging drop against a well buffer of 0.1 M HEPES pH 7.5, 15% PEG3350, 30% ethylene glycol, and 10% isopropanol. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.58 | 52.39 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 59.467 | α = 90 |
b = 79.883 | β = 90 |
c = 163.444 | 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 | 100 | CCD | Bruker AXIOM 200 | 2008-04-24 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X29A | 1.0 | NSLS | X29A |
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 | 1.8 | 81.72 | 94.6 | 8.8 | 13.2 | 69331 |
Refinement
Statistics | |||||||||||||||||||
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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 | THROUGHOUT | 1.8 | 30 | 65854 | 3389 | 94.17 | 0.1941 | 0.1931 | 0.2141 | RANDOM | 26.926 |
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] | |
-0.02 | 0.02 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.117 |
r_dihedral_angle_4_deg | 11.835 |
r_dihedral_angle_3_deg | 11.495 |
r_dihedral_angle_1_deg | 4.369 |
r_angle_refined_deg | 0.952 |
r_angle_other_deg | 0.744 |
r_chiral_restr | 0.054 |
r_bond_refined_d | 0.005 |
r_gen_planes_refined | 0.003 |
r_bond_other_d | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5271 |
Nucleic Acid Atoms | |
Solvent Atoms | 388 |
Heterogen Atoms | 49 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
DENZO | data reduction |
SCALEPACK | data scaling |
AMoRE | phasing |