1Y2B

Catalytic Domain Of Human Phosphodiesterase 4D In Complex With 3,5-dimethyl-1H-pyrazole-4-carboxylic acid ethyl ester


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7288PEG3350, ethylene glycol, isopropanol, glycerol and DTT, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 288K
Crystal Properties
Matthews coefficientSolvent content
2.4449.69

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.469α = 90
b = 79.009β = 90
c = 164.141γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93CCDADSC QUANTUM 210MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.3.11.1ALS8.3.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.481.6597.890.0489.46.8144200144200
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.41.436980.5882.64.59086

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.481.65144200144200762497.890.175720.175720.175210.18522RANDOM10.388
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]
0.920.03-0.95
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg2.66
r_scangle_it2.089
r_scbond_it1.25
r_angle_refined_deg1.065
r_angle_other_deg0.788
r_mcangle_it0.684
r_mcbond_it0.334
r_symmetry_vdw_other0.28
r_nbd_other0.223
r_nbd_refined0.212
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg2.66
r_scangle_it2.089
r_scbond_it1.25
r_angle_refined_deg1.065
r_angle_other_deg0.788
r_mcangle_it0.684
r_mcbond_it0.334
r_symmetry_vdw_other0.28
r_nbd_other0.223
r_nbd_refined0.212
r_symmetry_hbond_refined0.139
r_symmetry_vdw_refined0.108
r_xyhbond_nbd_refined0.107
r_nbtor_other0.08
r_chiral_restr0.07
r_bond_refined_d0.006
r_gen_planes_refined0.004
r_gen_planes_other0.004
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5253
Nucleic Acid Atoms
Solvent Atoms450
Heterogen Atoms104

Software

Software
Software NamePurpose
REFMACrefinement
Blu-Icedata collection
ELVESdata scaling
EPMRphasing