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Crystal structure of human PDE4a with 4-(3-butoxy-4-methoxyphenyl)methyl-2-imidazolidone
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QYK PDB entry 2QYK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 277 14-20%(w/v) PEG3350, 5-10%(v/v) glycerol, 100mM Tris-HCl, 200mM Magnesium acetate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.82 56.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.406 α = 90 b = 105.406 β = 90 c = 165.252 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 ADSC QUANTUM 315 double Si 111 crystal monochromator 2009-07-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
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 2.25 45.33 100 0.068 12.8 7.03 44862 2 40
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 2.25 2.33 100 0.326 4.3 7.11 4383
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 PDB entry 2QYK 2.25 45.33 42599 2262 99.94 0.18908 0.18732 0.185 0.22171 0.2198 RANDOM 38.352
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] -0.25 -0.25 0.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.571 r_dihedral_angle_4_deg 20.97 r_dihedral_angle_3_deg 15.237 r_dihedral_angle_1_deg 4.671 r_scangle_it 3.298 r_scbond_it 2.028 r_angle_refined_deg 1.297 r_mcangle_it 1.197 r_mcbond_it 0.598 r_chiral_restr 0.084
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.571 r_dihedral_angle_4_deg 20.97 r_dihedral_angle_3_deg 15.237 r_dihedral_angle_1_deg 4.671 r_scangle_it 3.298 r_scbond_it 2.028 r_angle_refined_deg 1.297 r_mcangle_it 1.197 r_mcbond_it 0.598 r_chiral_restr 0.084 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5406 Nucleic Acid Atoms Solvent Atoms 349 Heterogen Atoms 63
Software Software Software Name Purpose DNA data collection PHASER phasing REFMAC refinement CrystalClear data reduction CrystalClear data scaling