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PDE4 crystal structure in complex with small molecule inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TB7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 293 19% PEG 3350, 36 % Ethylene Glycol and 10 % Isopropanol as a precipitant
Crystal Properties Matthews coefficient Solvent content 2.59 52.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.444 α = 91.01 b = 78.347 β = 92.79 c = 161.756 γ = 90.08
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 293 IMAGE PLATE MARRESEARCH 2005-04-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE ENRAF-NONIUS FR571 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) 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 2.6 25 94.6 0.126 7 2.6 91922 7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.74 0.395
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 1TB7 2.61 25 82704 4409 94.77 0.1947 0.1913 0.1971 0.2583 0.2611 RANDOM 30.959
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] -0.01 0.18 0.37 0.15 -0.55 -0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.423 r_dihedral_angle_3_deg 17.812 r_dihedral_angle_4_deg 15.917 r_dihedral_angle_1_deg 5.525 r_angle_refined_deg 1.471 r_scangle_it 1.087 r_mcangle_it 1.05 r_scbond_it 0.718 r_mcbond_it 0.66 r_nbtor_refined 0.328
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.423 r_dihedral_angle_3_deg 17.812 r_dihedral_angle_4_deg 15.917 r_dihedral_angle_1_deg 5.525 r_angle_refined_deg 1.471 r_scangle_it 1.087 r_mcangle_it 1.05 r_scbond_it 0.718 r_mcbond_it 0.66 r_nbtor_refined 0.328 r_symmetry_hbond_refined 0.265 r_nbd_refined 0.257 r_symmetry_vdw_refined 0.243 r_xyhbond_nbd_refined 0.188 r_chiral_restr 0.1 r_metal_ion_refined 0.089 r_bond_refined_d 0.012 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20993 Nucleic Acid Atoms Solvent Atoms 210 Heterogen Atoms 240
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction SCALA data scaling