☰ Navigation Tabs
Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-425
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 2.64 53.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.939 α = 90 b = 110.812 β = 90 c = 160.983 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 2017-09-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97625 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 2.09 160.98 100 0.076 0.082 0.032 0.999 15.6 6.7 104009
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.09 2.134 100 0.835 0.352 0.742 2.2 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 2.1 91.28 98690 5318 99.98 0.17331 0.17073 0.1837 0.22216 0.2288 RANDOM 43.88
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] 0.56 -1.1 0.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.951 r_dihedral_angle_4_deg 18.31 r_dihedral_angle_3_deg 16.269 r_long_range_B_refined 8.765 r_long_range_B_other 8.765 r_scangle_other 7.235 r_dihedral_angle_1_deg 5.988 r_scbond_it 5.012 r_scbond_other 5.012 r_mcangle_it 4.874
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.951 r_dihedral_angle_4_deg 18.31 r_dihedral_angle_3_deg 16.269 r_long_range_B_refined 8.765 r_long_range_B_other 8.765 r_scangle_other 7.235 r_dihedral_angle_1_deg 5.988 r_scbond_it 5.012 r_scbond_other 5.012 r_mcangle_it 4.874 r_mcangle_other 4.874 r_mcbond_it 3.597 r_mcbond_other 3.597 r_angle_refined_deg 1.903 r_angle_other_deg 1.082 r_chiral_restr 0.203 r_bond_refined_d 0.018 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 10524 Nucleic Acid Atoms Solvent Atoms 575 Heterogen Atoms 448
Software Software Software Name Purpose REFMAC refinement XDS data reduction autoPROC data scaling PHASER phasing