☰ Navigation Tabs
Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-053
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 2.65 53.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.894 α = 90 b = 110.505 β = 90 c = 160.694 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 CRL 2016-04-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.976250 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 2.07 160.69 99.9 0.065 0.07 0.027 0.99 16.2 6.6 107710
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 2.07 2.08 94.8 0.794 0.859 0.327 0.75 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 2.08 91.22 102189 5443 99.78 0.17494 0.17248 0.2211 0.224 RANDOM 44.968
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] 0.4 -0.14 -0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.901 r_dihedral_angle_4_deg 19.538 r_dihedral_angle_3_deg 15.06 r_long_range_B_refined 8.76 r_long_range_B_other 8.76 r_scangle_other 6.977 r_dihedral_angle_1_deg 5.951 r_mcangle_it 4.919 r_mcangle_other 4.919 r_scbond_it 4.809
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.901 r_dihedral_angle_4_deg 19.538 r_dihedral_angle_3_deg 15.06 r_long_range_B_refined 8.76 r_long_range_B_other 8.76 r_scangle_other 6.977 r_dihedral_angle_1_deg 5.951 r_mcangle_it 4.919 r_mcangle_other 4.919 r_scbond_it 4.809 r_scbond_other 4.809 r_mcbond_it 3.806 r_mcbond_other 3.803 r_angle_refined_deg 1.653 r_angle_other_deg 1.377 r_chiral_restr 0.079 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.001 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 10524 Nucleic Acid Atoms Solvent Atoms 658 Heterogen Atoms 338
Software Software Software Name Purpose REFMAC refinement XDS data reduction autoPROC data scaling PHASER phasing