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Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-617
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 2.63 53.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.44 α = 90 b = 110.82 β = 90 c = 161.03 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 2015-12-07 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 1.79 66.94 100 0.084 0.099 0.052 0.99 13.5 6.7 165809
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 1.79 1.84 100 1.26 1.495 0.789 0.52 1.4 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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3SL3 1.79 66.94 157351 8357 99.97 0.1682 0.1667 0.1796 0.1967 0.2062 RANDOM 30.396
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] 0.37 -1.03 0.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.465 r_dihedral_angle_4_deg 20.046 r_dihedral_angle_3_deg 14.264 r_dihedral_angle_1_deg 5.706 r_angle_refined_deg 1.638 r_angle_other_deg 1.468 r_chiral_restr 0.093 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.465 r_dihedral_angle_4_deg 20.046 r_dihedral_angle_3_deg 14.264 r_dihedral_angle_1_deg 5.706 r_angle_refined_deg 1.638 r_angle_other_deg 1.468 r_chiral_restr 0.093 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10520 Nucleic Acid Atoms Solvent Atoms 878 Heterogen Atoms 542
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction xia2 data reduction XSCALE data scaling PHASER phasing