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The structure of PDE4A with pentoxifylline at 2.84A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3I8V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.25 293 2ul of 34mg/ml protein in HEPES pH 7.5 150mM NaCl, 5mM DTT with 2ul of 1.5mM Ammonium sulfate, 0.1 M Bis/Tris propane , VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.9 57.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.938 α = 90 b = 104.938 β = 90 c = 163.652 γ = 90
Symmetry Space Group P 41 21 2
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 RAYONIX MX-225 2010-11-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.979 APS 21-ID-F
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 2.84 48.4 100 0.068 34.4 9.6 22313 22313 -4
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 2.84 2.94 100 0.578 4.5 9.9
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 3I8V 2.84 48.4 21117 1136 100 0.22388 0.22048 0.208 0.28951 0.2702 RANDOM 70.118
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.591 r_dihedral_angle_4_deg 16.909 r_dihedral_angle_3_deg 16.002 r_dihedral_angle_1_deg 4.429 r_scangle_it 1.507 r_angle_refined_deg 1.003 r_mcangle_it 0.899 r_scbond_it 0.887 r_mcbond_it 0.473 r_chiral_restr 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.591 r_dihedral_angle_4_deg 16.909 r_dihedral_angle_3_deg 16.002 r_dihedral_angle_1_deg 4.429 r_scangle_it 1.507 r_angle_refined_deg 1.003 r_mcangle_it 0.899 r_scbond_it 0.887 r_mcbond_it 0.473 r_chiral_restr 0.07 r_bond_refined_d 0.007 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5383 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 54
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling