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Catalytic Domain Of Human Phosphodiesterase 4D In Complex With Cilomilast
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 288 PEG3350, ethylene glycol, isopropanol, glycerol and DTT, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 288K
Crystal Properties Matthews coefficient Solvent content 2.44 49.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.486 α = 90 b = 78.966 β = 90 c = 164.186 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 93 CCD ADSC QUANTUM 210 2003-09-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.1 ALS 8.3.1
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 1.55 81.65 99.1 0.097 12.5 3.8 107956 107956
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) 1.55 1.59 99.9 0.261 2.5 3.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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 1.55 81.65 107956 107956 5683 99.08 0.18387 0.18276 0.238 0.20498 0.2585 RANDOM 13.768
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] 0.23 -0.43 0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 2.667 r_scangle_it 2.516 r_scbond_it 1.515 r_angle_refined_deg 1.093 r_mcangle_it 0.939 r_angle_other_deg 0.782 r_mcbond_it 0.475 r_symmetry_vdw_other 0.293 r_nbd_other 0.219 r_nbd_refined 0.204
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 2.667 r_scangle_it 2.516 r_scbond_it 1.515 r_angle_refined_deg 1.093 r_mcangle_it 0.939 r_angle_other_deg 0.782 r_mcbond_it 0.475 r_symmetry_vdw_other 0.293 r_nbd_other 0.219 r_nbd_refined 0.204 r_xyhbond_nbd_refined 0.117 r_symmetry_hbond_refined 0.113 r_symmetry_vdw_refined 0.088 r_nbtor_other 0.08 r_chiral_restr 0.07 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_gen_planes_other 0.003 r_bond_other_d 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_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 5288 Nucleic Acid Atoms Solvent Atoms 596 Heterogen Atoms 184
Software Software Software Name Purpose REFMAC refinement Blu-Ice data collection ELVES data scaling EPMR phasing