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Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-1335
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 pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.62 53.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.465 α = 90 b = 110.848 β = 90 c = 160.461 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 1.99 80.19 100 0.066 0.071 0.028 0.999 14.1 6.5 120894
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 1.99 2.04 100 0.79 0.859 0.333 0.589 2 6.6
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 1.99 80.19 112544 5954 97.94 0.20108 0.19819 0.211 0.25539 0.2633 RANDOM 43.247
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] 0.76 -1.23 0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.694 r_dihedral_angle_4_deg 17.094 r_dihedral_angle_3_deg 16.23 r_long_range_B_refined 8.936 r_long_range_B_other 8.935 r_scangle_other 6.605 r_dihedral_angle_1_deg 6.269 r_mcangle_it 5.206 r_mcangle_other 5.206 r_scbond_it 4.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.694 r_dihedral_angle_4_deg 17.094 r_dihedral_angle_3_deg 16.23 r_long_range_B_refined 8.936 r_long_range_B_other 8.935 r_scangle_other 6.605 r_dihedral_angle_1_deg 6.269 r_mcangle_it 5.206 r_mcangle_other 5.206 r_scbond_it 4.71 r_scbond_other 4.709 r_mcbond_it 3.896 r_mcbond_other 3.896 r_angle_refined_deg 1.935 r_angle_other_deg 1.115 r_chiral_restr 0.132 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 10485 Nucleic Acid Atoms Solvent Atoms 590 Heterogen Atoms 455
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling Coot model building