4MYQ
Selective Inhibition of the Catalytic Domain Of Human Phosphodiesterase 4B With A-33
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3G45 | PDB entry 3G45 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 289 | VCID6271 PDE4 AT 7.9 MG/ML IN 20MM HEPES PH 7.5, 100 MM NACL, 1MM DTT, WITH 0.5MM A-33 AGAINST JCSG_ A10 (OPTIMIZATION SCREEN), 328.57MM POTASSIUM FORMATE, 24% W/V PEG 3350, CRYO 20% ETHYLENE GLYCOL AND 0.1MM COMPOUND, CRYSTAL TRACKING ID 232128E12, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K, temperature 289.0K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.73 | 54.93 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 99.7 | α = 90 |
b = 99.7 | β = 90 |
c = 47.02 | γ = 90 |
Symmetry | |
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Space Group | P 42 |
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 | RIGAKU SATURN 944+ | 2012-03-21 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU | 1.5418 |
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 | 1.9 | 49.85 | 97.3 | 0.087 | 12.5 | 3.2 | 36759 | 35759 | 2 | -3 | 18.71 |
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 | 1.9 | 1.95 | 86.7 | 0.483 | 2.3 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | 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 | PDB entry 3G45 | 1.9 | 49.85 | 2 | 36759 | 35759 | 1788 | 97.3 | 0.19 | 0.188 | 0.222 | RANDOM | 12.8 |
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] | |
0.12 | 0.12 | -0.25 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.805 |
r_dihedral_angle_4_deg | 19.018 |
r_dihedral_angle_3_deg | 13.778 |
r_dihedral_angle_1_deg | 5.002 |
r_angle_refined_deg | 1.487 |
r_angle_other_deg | 1.013 |
r_chiral_restr | 0.084 |
r_bond_refined_d | 0.014 |
r_gen_planes_refined | 0.007 |
r_gen_planes_other | 0.006 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2758 |
Nucleic Acid Atoms | |
Solvent Atoms | 375 |
Heterogen Atoms | 41 |
Software
Software | |
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Software Name | Purpose |
PHASER | phasing |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |