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Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-007
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3SL3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 24% PEG 3350, 30% Ethylene Glycol, 0.1 M HEPES
Crystal Properties Matthews coefficient Solvent content 2.65 53.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.11 α = 90 b = 110.717 β = 90 c = 161.49 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M-F 2018-02-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91587 Diamond I04-1
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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.78 65.23 100 0.061 0.067 0.026 0.999 15 6.4 170039
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) Redundancy Number Unique Reflections (All) 1 1.78 1.83 100 0.684 0.759 0.323 0.725 2 5.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (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 Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3SL3 1.78 65.23 160321 8380 99.24 0.17909 0.17724 0.1895 0.21436 0.2221 RANDOM 31.367
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 -1.13 0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.14 r_dihedral_angle_4_deg 19.693 r_dihedral_angle_3_deg 14.61 r_long_range_B_refined 7.661 r_long_range_B_other 7.661 r_scangle_other 6.088 r_dihedral_angle_1_deg 5.548 r_scbond_it 4.109 r_scbond_other 4.109 r_mcangle_it 3.685
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.14 r_dihedral_angle_4_deg 19.693 r_dihedral_angle_3_deg 14.61 r_long_range_B_refined 7.661 r_long_range_B_other 7.661 r_scangle_other 6.088 r_dihedral_angle_1_deg 5.548 r_scbond_it 4.109 r_scbond_other 4.109 r_mcangle_it 3.685 r_mcangle_other 3.685 r_mcbond_other 2.716 r_mcbond_it 2.715 r_angle_refined_deg 1.9 r_angle_other_deg 1.099 r_chiral_restr 0.156 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 Atoms Number Protein Atoms 10531 Nucleic Acid Atoms Solvent Atoms 941 Heterogen Atoms 494
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing DIALS data collection