3KKT
Crystal structure of human PDE4b with 5-[3-[(1S,2S,4R)-Bicyclo[2.2.1]hept-2-yloxy]-4-methoxyp henyl]tetrahydro-2(1H)-pyrimidinone reveals ordering of the C-terminal helix residues 502-509.
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 294 | 1.2 M tri-Sodium citrate dihydrate, 0.1 M BisTris propane pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.15 | 42.73 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 89.74 | α = 90 |
b = 89.74 | β = 90 |
c = 337.443 | γ = 120 |
Symmetry | |
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Space Group | P 65 2 2 |
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 | ADSC QUANTUM 315 | Si (111) double crystal monochromator. Kirkpatrick Baez bimorph mirror pair for horizontal and vertical focussing | 2009-08-12 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I02 | 0.9759 | Diamond | I02 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym 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 | 2.475 | 70.588 | 99.8 | 0.104 | 5.2 | 6.2 | 29905 | 2 | 46.3 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.48 | 2.54 | 99.7 | 0.366 | 2.1 | 6.4 | 4237 |
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 | PDB entry 1XLZ chain A | 2.48 | 70.588 | 28393 | 1512 | 99.79 | 0.23757 | 0.23461 | 0.29473 | RANDOM | 42.455 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
-0.43 | -0.22 | -0.43 | 0.65 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.501 |
r_dihedral_angle_3_deg | 17.218 |
r_dihedral_angle_4_deg | 16.432 |
r_dihedral_angle_1_deg | 4.696 |
r_scangle_it | 1.389 |
r_angle_refined_deg | 1.071 |
r_scbond_it | 0.809 |
r_mcangle_it | 0.655 |
r_mcbond_it | 0.339 |
r_chiral_restr | 0.076 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5547 |
Nucleic Acid Atoms | |
Solvent Atoms | 60 |
Heterogen Atoms | 69 |
Software
Software | |
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Software Name | Purpose |
DNA | data collection |
PHASER | phasing |
REFMAC | refinement |
CrystalClear | data reduction |
SCALA | data scaling |