☰ Navigation Tabs
Crystal structure of PDE4D2 in complex with inhibitor (S_Zl-n-91)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 7.5 277 The ~10mg/ml PDE4D2 (86-413) was stored in a buffer of 20 mM Tris.base, pH 7.5, 50 mM NaCl, 1 mM 2-mercaptoethanol, 1 mM EDTA and mixed with 2 mM (R)- or (S)-5. They were crystallized at 4C by hanging drop against a well buffer of 0.1 M HEPES pH 7.5, 15% PEG3350, 30% ethylene glycol, and 10% isopropanol.
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.948 α = 90 b = 80.197 β = 90 c = 163.67 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 Bruker AXIOM 200 2008-04-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.0 NSLS X29A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.6 81 93.1 0.068 10.5 12.6 95949
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 THROUGHOUT 1.6 30 91110 4724 92.97 0.20707 0.20619 0.2147 0.2243 0.2295 RANDOM 28.358
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] 0.06 -0.03 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.389 r_dihedral_angle_3_deg 11.024 r_dihedral_angle_4_deg 9.374 r_dihedral_angle_1_deg 4.268 r_long_range_B_refined 3.98 r_long_range_B_other 3.759 r_scangle_other 2.021 r_mcangle_it 1.648 r_mcangle_other 1.648 r_scbond_it 1.211
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.389 r_dihedral_angle_3_deg 11.024 r_dihedral_angle_4_deg 9.374 r_dihedral_angle_1_deg 4.268 r_long_range_B_refined 3.98 r_long_range_B_other 3.759 r_scangle_other 2.021 r_mcangle_it 1.648 r_mcangle_other 1.648 r_scbond_it 1.211 r_scbond_other 1.21 r_mcbond_it 0.977 r_mcbond_other 0.976 r_angle_refined_deg 0.924 r_angle_other_deg 0.734 r_chiral_restr 0.05 r_bond_refined_d 0.005 r_gen_planes_refined 0.003 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 5271 Nucleic Acid Atoms Solvent Atoms 384 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing