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PDE4D 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 2.64 53.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.967 α = 90 b = 79.739 β = 90 c = 163.845 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 293 CCD MARRESEARCH 2007-06-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE OTHER 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 1.99 20 94.7 0.1 1.7 3.1 245085
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 1.99 2.1 0.59
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1TB7 1.99 20 49055 2627 94.52 0.2229 0.2198 0.2813 0.2647 RANDOM 30.36
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] 1.93 -0.06 -1.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.862 r_dihedral_angle_3_deg 15.87 r_dihedral_angle_4_deg 13.72 r_dihedral_angle_1_deg 6.089 r_scangle_it 3.757 r_scbond_it 2.849 r_angle_refined_deg 1.848 r_mcangle_it 1.695 r_mcbond_it 1.19 r_nbtor_refined 0.296
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.862 r_dihedral_angle_3_deg 15.87 r_dihedral_angle_4_deg 13.72 r_dihedral_angle_1_deg 6.089 r_scangle_it 3.757 r_scbond_it 2.849 r_angle_refined_deg 1.848 r_mcangle_it 1.695 r_mcbond_it 1.19 r_nbtor_refined 0.296 r_symmetry_vdw_refined 0.259 r_symmetry_hbond_refined 0.237 r_nbd_refined 0.219 r_xyhbond_nbd_refined 0.191 r_chiral_restr 0.127 r_metal_ion_refined 0.106 r_bond_refined_d 0.022 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5207 Nucleic Acid Atoms Solvent Atoms 471 Heterogen Atoms 184
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction SCALA data scaling