☰ Navigation Tabs
Crystal structure of PDE4B catalytic domain in complex with a pyrazolopyridine inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1F0J PDB ENTRY 1F0J (Molecule A)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 14-18% PEG 3000, 10% Glycerol, 50mM Sodium Cacodylate pH 6.5, 100mM Sodium Acetate, 1M Sodium Chloride, 1% DMF, 5mM DTT, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.73 54.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.448 α = 90 b = 94.725 β = 90 c = 105.671 γ = 90
Symmetry Space Group I 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 4 2002-10-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.9326 ESRF ID14-4
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 1.75 25 98.4 0.062 10.9 44609 23.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.75 1.81 97.4 0.451 2.5 4351
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 THROUGHOUT PDB ENTRY 1F0J (Molecule A) 1.75 20 44290 2235 100 0.201 0.199 0.1976 0.241 0.2384 RANDOM 30.138
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] -1.87 -0.36 2.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.192 r_dihedral_angle_4_deg 26.357 r_dihedral_angle_3_deg 14.419 r_scangle_it 5.109 r_dihedral_angle_1_deg 4.926 r_scbond_it 3.605 r_mcangle_it 2.811 r_mcbond_it 2.047 r_angle_refined_deg 1.363 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.192 r_dihedral_angle_4_deg 26.357 r_dihedral_angle_3_deg 14.419 r_scangle_it 5.109 r_dihedral_angle_1_deg 4.926 r_scbond_it 3.605 r_mcangle_it 2.811 r_mcbond_it 2.047 r_angle_refined_deg 1.363 r_nbtor_refined 0.306 r_nbd_refined 0.218 r_xyhbond_nbd_refined 0.179 r_symmetry_vdw_refined 0.177 r_symmetry_hbond_refined 0.149 r_chiral_restr 0.097 r_metal_ion_refined 0.026 r_bond_refined_d 0.015 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2714 Nucleic Acid Atoms Solvent Atoms 303 Heterogen Atoms 34
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction AMoRE phasing