6FT0

Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-425


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 pH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.6453.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 98.939α = 90
b = 110.812β = 90
c = 160.983γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6MCRL2017-09-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.97625DiamondI03

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
12.09160.981000.0760.0820.0320.99915.66.7104009
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.092.1341000.8350.3520.7422.26.6

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 REPLACEMENTTHROUGHOUT3SL32.191.2898690531899.980.173310.170730.22216RANDOM43.88
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]
0.56-1.10.54
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.951
r_dihedral_angle_4_deg18.31
r_dihedral_angle_3_deg16.269
r_long_range_B_refined8.765
r_long_range_B_other8.765
r_scangle_other7.235
r_dihedral_angle_1_deg5.988
r_scbond_it5.012
r_scbond_other5.012
r_mcangle_it4.874
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.951
r_dihedral_angle_4_deg18.31
r_dihedral_angle_3_deg16.269
r_long_range_B_refined8.765
r_long_range_B_other8.765
r_scangle_other7.235
r_dihedral_angle_1_deg5.988
r_scbond_it5.012
r_scbond_other5.012
r_mcangle_it4.874
r_mcangle_other4.874
r_mcbond_it3.597
r_mcbond_other3.597
r_angle_refined_deg1.903
r_angle_other_deg1.082
r_chiral_restr0.203
r_bond_refined_d0.018
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 Atoms10524
Nucleic Acid Atoms
Solvent Atoms575
Heterogen Atoms448

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing