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Catalytic Domain Of Human Phosphodiesterase 4D In Complex With Zardaverine
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 2.41 48.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.279 α = 90 b = 78.401 β = 90 c = 163.471 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 2003-08-28 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 1.54 81.65 97.94 0.065 6 3.4 107189 107189
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 1.54 1.58 93.6 0.51 1.5 2.9 7973
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 1.54 81.65 107189 107189 5629 97.94 0.17923 0.17839 0.1922 0.19491 0.207 RANDOM 10.845
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] 0.8 0.03 -0.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 2.734 r_scangle_it 2.403 r_scbond_it 1.479 r_angle_refined_deg 1.116 r_angle_other_deg 1.01 r_mcangle_it 0.778 r_mcbond_it 0.375 r_symmetry_vdw_other 0.274 r_nbd_other 0.225 r_nbd_refined 0.206
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 2.734 r_scangle_it 2.403 r_scbond_it 1.479 r_angle_refined_deg 1.116 r_angle_other_deg 1.01 r_mcangle_it 0.778 r_mcbond_it 0.375 r_symmetry_vdw_other 0.274 r_nbd_other 0.225 r_nbd_refined 0.206 r_symmetry_hbond_refined 0.148 r_symmetry_vdw_refined 0.141 r_xyhbond_nbd_refined 0.132 r_nbtor_other 0.081 r_chiral_restr 0.079 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_gen_planes_other 0.005 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 5253 Nucleic Acid Atoms Solvent Atoms 653 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement Blu-Ice data collection ELVES data scaling EPMR phasing