6FTW

Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-048


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
2.6553.55

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 99.14α = 90
b = 111.43β = 90
c = 160.06γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-FCRL2015-11-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.97949DiamondI04

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
12.166599.90.0850.0920.0350.99914.56.795516
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)
12.162.2299.81.0631.1530.4450.6231.76.6

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 REPLACEMENTTHROUGHOUT3SL32.166590714472999.880.18450.181940.23314RANDOM47.953
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]
0.56-1.120.56
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.182
r_dihedral_angle_4_deg19.212
r_dihedral_angle_3_deg15.593
r_long_range_B_refined8.333
r_long_range_B_other8.332
r_scangle_other6.976
r_dihedral_angle_1_deg5.867
r_mcangle_it5.383
r_mcangle_other5.383
r_scbond_it4.797
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.182
r_dihedral_angle_4_deg19.212
r_dihedral_angle_3_deg15.593
r_long_range_B_refined8.333
r_long_range_B_other8.332
r_scangle_other6.976
r_dihedral_angle_1_deg5.867
r_mcangle_it5.383
r_mcangle_other5.383
r_scbond_it4.797
r_scbond_other4.796
r_mcbond_it3.887
r_mcbond_other3.885
r_angle_refined_deg1.761
r_angle_other_deg1.091
r_chiral_restr0.105
r_bond_refined_d0.017
r_gen_planes_refined0.008
r_bond_other_d0.003
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 Atoms10555
Nucleic Acid Atoms
Solvent Atoms551
Heterogen Atoms348

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing