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Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-226
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 2.65 53.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.804 α = 90 b = 111.042 β = 90 c = 161.089 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 CRL 2015-11-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97949 Diamond I04
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 1.9 67.1 100 0.105 0.114 0.044 0.996 11.8 6.8 139841
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 1.9 1.93 100 1.16 1.26 0.488 0.62 1.6 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 1.9 67.1 132610 7136 99.99 0.17493 0.17357 0.1859 0.19998 0.2117 RANDOM 31.576
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] 0.2 -0.56 0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.235 r_dihedral_angle_4_deg 18.324 r_dihedral_angle_3_deg 13.473 r_long_range_B_refined 6.917 r_long_range_B_other 6.917 r_scangle_other 5.303 r_dihedral_angle_1_deg 5.097 r_scbond_it 3.559 r_scbond_other 3.559 r_mcangle_it 3.383
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.235 r_dihedral_angle_4_deg 18.324 r_dihedral_angle_3_deg 13.473 r_long_range_B_refined 6.917 r_long_range_B_other 6.917 r_scangle_other 5.303 r_dihedral_angle_1_deg 5.097 r_scbond_it 3.559 r_scbond_other 3.559 r_mcangle_it 3.383 r_mcangle_other 3.383 r_mcbond_it 2.463 r_mcbond_other 2.463 r_angle_refined_deg 1.599 r_angle_other_deg 1.037 r_chiral_restr 0.1 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 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 10542 Nucleic Acid Atoms Solvent Atoms 831 Heterogen Atoms 482
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing