6FW3

Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-007


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3SL3 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529324% PEG 3350, 30% Ethylene Glycol, 0.1 M HEPES
Crystal Properties
Matthews coefficientSolvent content
2.6553.65

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 99.11α = 90
b = 110.717β = 90
c = 161.49γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2018-02-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.91587DiamondI04-1

Data Collection

Overall
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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.7865.231000.0610.0670.0260.999156.4170039
Highest Resolution Shell
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)RedundancyNumber Unique Reflections (All)
11.781.831000.6840.7590.3230.72525.5

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3SL31.7865.23160321838099.240.179090.177240.21436RANDOM31.367
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]
0.69-1.130.44
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.14
r_dihedral_angle_4_deg19.693
r_dihedral_angle_3_deg14.61
r_long_range_B_refined7.661
r_long_range_B_other7.661
r_scangle_other6.088
r_dihedral_angle_1_deg5.548
r_scbond_it4.109
r_scbond_other4.109
r_mcangle_it3.685
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.14
r_dihedral_angle_4_deg19.693
r_dihedral_angle_3_deg14.61
r_long_range_B_refined7.661
r_long_range_B_other7.661
r_scangle_other6.088
r_dihedral_angle_1_deg5.548
r_scbond_it4.109
r_scbond_other4.109
r_mcangle_it3.685
r_mcangle_other3.685
r_mcbond_other2.716
r_mcbond_it2.715
r_angle_refined_deg1.9
r_angle_other_deg1.099
r_chiral_restr0.156
r_bond_refined_d0.019
r_gen_planes_refined0.009
r_bond_other_d0.002
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10531
Nucleic Acid Atoms
Solvent Atoms941
Heterogen Atoms494

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
DIALSdata collection