5ZZ2
Crystal structure of PDE5 in complex with inhibitor LW1634
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4MD6 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 298 | 0.1M Cacodylate Sodium (pH 6.5), 0.2 M MgSO4, 18% PEG3350, 2.5% ethanol |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.07 | 59.97 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 74.474 | α = 90 |
b = 74.474 | β = 90 |
c = 132.341 | γ = 120 |
Symmetry | |
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Space Group | P 31 2 1 |
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 | OXFORD ONYX CCD | 2018-02-05 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SEALED TUBE | OXFORD DIFFRACTION ENHANCE ULTRA | 1.5406 |
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 | 2.6 | 24.73 | 99.29 | 27.7 | 7.6 | 13486 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1 | 2.6 | 2.7 |
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 | 4MD6 | 2.6 | 24.73 | 12789 | 697 | 99.13 | 0.21153 | 0.20865 | 0.26436 | RANDOM | 47.714 |
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] | |
0.03 | 0.01 | 0.03 | -0.08 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 38.282 |
r_dihedral_angle_3_deg | 14.387 |
r_dihedral_angle_4_deg | 10.771 |
r_long_range_B_refined | 6.05 |
r_dihedral_angle_1_deg | 5.493 |
r_long_range_B_other | 5.393 |
r_mcangle_it | 3.301 |
r_mcangle_other | 3.3 |
r_scangle_other | 3.162 |
r_mcbond_it | 1.908 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2418 |
Nucleic Acid Atoms | |
Solvent Atoms | 41 |
Heterogen Atoms | 37 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
CrysalisPro | data reduction |
CrysalisPro | data scaling |
PHASER | phasing |