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Crystal structure of chimeric PDE5/PDE6 catalytic domain complexed with sildenafil
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2H42 PDB entry 2H42
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 277 100 mM Tris, 200 mM MgSO4, 12% PEG-3350, 2.5% ethanol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.73 54.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.732 α = 90 b = 109.825 β = 90 c = 199.668 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 CCD ADSC QUANTUM 210 2006-10-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.0 APS 17-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.87 29.8 86.68 31941 31941
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.873 2.947 72.34
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB entry 2H42 2.87 23.08 31941 31941 1655 86.68 0.22588 0.22588 0.22337 0.2185 0.27528 0.2684 RANDOM 23.415
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] -0.38 1.25 -0.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.51 r_dihedral_angle_3_deg 18.705 r_dihedral_angle_4_deg 16.846 r_dihedral_angle_1_deg 5.51 r_scangle_it 2.953 r_scbond_it 1.688 r_angle_refined_deg 1.512 r_mcangle_it 0.961 r_mcbond_it 0.433 r_chiral_restr 0.105
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.51 r_dihedral_angle_3_deg 18.705 r_dihedral_angle_4_deg 16.846 r_dihedral_angle_1_deg 5.51 r_scangle_it 2.953 r_scbond_it 1.688 r_angle_refined_deg 1.512 r_mcangle_it 0.961 r_mcbond_it 0.433 r_chiral_restr 0.105 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10570 Nucleic Acid Atoms Solvent Atoms 13 Heterogen Atoms 140
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement d*TREK data reduction d*TREK data scaling