6FET | pdb_00006fet

Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-1439


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529324% PEG 3350, 30% Ethylene Glycol, 0.1 M HEPES
Crystal Properties
Matthews coefficientSolvent content
2.652.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 97.19α = 90
b = 110.71β = 90
c = 161.48γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6MCRL2017-02-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.97624DiamondI03

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
11.8855.351000.0850.0920.0350.99913.76.7141825
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)
11.881.931001.7271.8750.7260.4981.26.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT1.8855.35134495723499.920.172910.171480.180.199320.21RANDOM40.058
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]
-0.1-1.891.98
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.927
r_dihedral_angle_4_deg19.254
r_dihedral_angle_3_deg13.597
r_long_range_B_refined8.128
r_long_range_B_other8.128
r_scangle_other7.006
r_scbond_it5.126
r_scbond_other5.126
r_dihedral_angle_1_deg5.073
r_mcangle_it4.344
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.927
r_dihedral_angle_4_deg19.254
r_dihedral_angle_3_deg13.597
r_long_range_B_refined8.128
r_long_range_B_other8.128
r_scangle_other7.006
r_scbond_it5.126
r_scbond_other5.126
r_dihedral_angle_1_deg5.073
r_mcangle_it4.344
r_mcangle_other4.344
r_mcbond_it3.466
r_mcbond_other3.466
r_angle_refined_deg1.881
r_angle_other_deg1.088
r_chiral_restr0.112
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 Atoms10515
Nucleic Acid Atoms
Solvent Atoms625
Heterogen Atoms583

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing