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Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-1086
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 2.51 50.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.068 α = 90 b = 158.233 β = 90 c = 111.405 γ = 90
Symmetry Space Group C 2 2 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 PILATUS3 6M CRL 2016-09-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97622 Diamond I03
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 1.928 81.491 99.1 0.061 0.066 0.026 0.999 19.3 6.6 62982
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 1.928 1.961 99.5 0.844 0.913 0.345 0.723 2.2 6.8
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3SL3 1.93 81.49 59752 3200 99.09 0.16173 0.1599 0.19608 0.1957 RANDOM 39.066
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] -0.41 0.89 -0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.033 r_dihedral_angle_4_deg 16.354 r_dihedral_angle_3_deg 15.485 r_long_range_B_refined 8.491 r_long_range_B_other 8.491 r_scangle_other 6.164 r_dihedral_angle_1_deg 5.66 r_mcangle_it 4.284 r_mcangle_other 4.284 r_scbond_it 3.972
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.033 r_dihedral_angle_4_deg 16.354 r_dihedral_angle_3_deg 15.485 r_long_range_B_refined 8.491 r_long_range_B_other 8.491 r_scangle_other 6.164 r_dihedral_angle_1_deg 5.66 r_mcangle_it 4.284 r_mcangle_other 4.284 r_scbond_it 3.972 r_scbond_other 3.971 r_mcbond_it 3.007 r_mcbond_other 2.998 r_angle_refined_deg 1.625 r_angle_other_deg 1.037 r_chiral_restr 0.101 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 5246 Nucleic Acid Atoms Solvent Atoms 302 Heterogen Atoms 224
Software Software Software Name Purpose REFMAC refinement XDS data reduction autoPROC data scaling PHASER phasing