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Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-001
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 2.63 53.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.223 α = 90 b = 111.092 β = 90 c = 160.798 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 PILATUS3 6M CRL 2016-04-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97623 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.25 160.8 96.4 0.113 0.998 13.8 6.5 80611
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.25 2.38 100 0.763 2.6 6.5
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3SL3 2.25 91.4 76504 4023 96.37 0.1754 0.17365 0.20965 0.1997 RANDOM 45.341
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] 1.17 -2.19 1.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.563 r_dihedral_angle_4_deg 20.26 r_dihedral_angle_3_deg 15.572 r_long_range_B_refined 9.564 r_long_range_B_other 9.564 r_scangle_other 7.753 r_mcangle_it 5.325 r_mcangle_other 5.325 r_scbond_it 5.185 r_scbond_other 5.184
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.563 r_dihedral_angle_4_deg 20.26 r_dihedral_angle_3_deg 15.572 r_long_range_B_refined 9.564 r_long_range_B_other 9.564 r_scangle_other 7.753 r_mcangle_it 5.325 r_mcangle_other 5.325 r_scbond_it 5.185 r_scbond_other 5.184 r_dihedral_angle_1_deg 5.18 r_mcbond_it 3.795 r_mcbond_other 3.795 r_angle_refined_deg 1.699 r_angle_other_deg 1.649 r_chiral_restr 0.104 r_bond_refined_d 0.015 r_bond_other_d 0.01 r_gen_planes_refined 0.01 r_gen_planes_other 0.008 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 10526 Nucleic Acid Atoms Solvent Atoms 553 Heterogen Atoms 360
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing