- PDB-4y87: Crystal structure of phosphodiesterase 9 in complex with (R)-C33 ... -
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Basic information
Entry
Database: PDB / ID: 4y87
Title
Crystal structure of phosphodiesterase 9 in complex with (R)-C33 (6-{[(1R)-1-(4-chlorophenyl)ethyl]amino}-1-cyclopentyl-1,5-dihydro-4H-pyrazolo[3,4-d]pyrimidin-4-one)
Components
High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A
Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION
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Sample preparation
Crystal
Density Matthews: 3.04 Å3/Da / Density % sol: 59.5 %
Crystal grow
Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: The PDE9A2 (8-10 mg/mL) in a buffer of 50 mM NaCl, 20 mM Tris-HCl, pH 7.5, 1 mM mercaptoethanol, and 1 mM EDTA was mixed with 2 mM C33 or (R)-C33 and crystallized against a well buffer of 1. ...Details: The PDE9A2 (8-10 mg/mL) in a buffer of 50 mM NaCl, 20 mM Tris-HCl, pH 7.5, 1 mM mercaptoethanol, and 1 mM EDTA was mixed with 2 mM C33 or (R)-C33 and crystallized against a well buffer of 1.8 - 2.0 M sodium formate.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1.05 Å / Relative weight: 1
Reflection
Resolution: 3.1→98.22 Å / Num. obs: 24552 / % possible obs: 84.9 % / Redundancy: 6.6 % / Net I/σ(I): 7.6
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Processing
Software
Name
Version
Classification
REFMAC
5.8.0073
refinement
HKL-2000
datareduction
HKL-2000
datascaling
PHASER
phasing
Refinement
Resolution: 3.1→98.22 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.901 / SU B: 15.792 / SU ML: 0.257 / Cross valid method: THROUGHOUT / ESU R: 1.249 / ESU R Free: 0.396 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.24742
1162
4.7 %
RANDOM
Rwork
0.20518
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obs
0.20719
23302
84.62 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK