6RCW
Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-053
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3SL3 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 293 | 24% PEG 3350, 30% Ethylene glycol, 0.1 M HEPES pH 7.5 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.65 | 53.7 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 99.894 | α = 90 |
b = 110.505 | β = 90 |
c = 160.694 | 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 | PIXEL | DECTRIS PILATUS 6M | CRL | 2016-04-09 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I03 | 0.976250 | Diamond | I03 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | 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 | 2.07 | 160.69 | 99.9 | 0.065 | 0.07 | 0.027 | 0.99 | 16.2 | 6.6 | 107710 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 2.07 | 2.08 | 94.8 | 0.794 | 0.859 | 0.327 | 0.75 | 2 | 6.8 |
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 | 3SL3 | 2.08 | 91.22 | 102189 | 5443 | 99.78 | 0.17494 | 0.17248 | 0.2211 | RANDOM | 44.968 |
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] | |
0.4 | -0.14 | -0.26 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.901 |
r_dihedral_angle_4_deg | 19.538 |
r_dihedral_angle_3_deg | 15.06 |
r_long_range_B_refined | 8.76 |
r_long_range_B_other | 8.76 |
r_scangle_other | 6.977 |
r_dihedral_angle_1_deg | 5.951 |
r_mcangle_it | 4.919 |
r_mcangle_other | 4.919 |
r_scbond_it | 4.809 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 10524 |
Nucleic Acid Atoms | |
Solvent Atoms | 658 |
Heterogen Atoms | 338 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
autoPROC | data scaling |
PHASER | phasing |