3O56

Catalytic domain of human phosphodiesterase 4b2b in complex with a 5-heterocycle pyrazolopyridine inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3D3P 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.527714-18% PEG 3000, 10% Glycerol, 50mM Sodium Cacodylate pH 6.5, 100mM Sodium Acetate, 1M Sodium Chloride, 1% DMF, 5mM DTT, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.7154.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 88.531α = 90
b = 94.592β = 90
c = 105.089γ = 90
Symmetry
Space GroupI 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42004-02-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-40.9393ESRFID14-4

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.4229.70399.60.0940.09416.57.21711752.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.422.481000.3790.37927.31253

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT3D3P2.4220170978651000.19930.19620.2601RANDOM57.0208
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]
-6.19-3.219.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.595
r_dihedral_angle_3_deg16.163
r_dihedral_angle_4_deg15.043
r_scangle_it5.611
r_dihedral_angle_1_deg4.937
r_scbond_it3.722
r_mcangle_it3.066
r_mcbond_it1.741
r_angle_refined_deg1.325
r_angle_other_deg0.905
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.595
r_dihedral_angle_3_deg16.163
r_dihedral_angle_4_deg15.043
r_scangle_it5.611
r_dihedral_angle_1_deg4.937
r_scbond_it3.722
r_mcangle_it3.066
r_mcbond_it1.741
r_angle_refined_deg1.325
r_angle_other_deg0.905
r_mcbond_other0.464
r_chiral_restr0.078
r_bond_refined_d0.014
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2705
Nucleic Acid Atoms
Solvent Atoms124
Heterogen Atoms48

Software

Software
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
REFMACphasing