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Crystal structure of human phosphodiesterase 4d with roflumilast
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 293 100MM HEPES PH 7.5, 35% ETHYLENE GLYCOL, 5% GLYCEROL, 22% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.58 52.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.665 α = 90 b = 111.952 β = 90 c = 161.701 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 100 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 ALS 5.0.1
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 2.5 50 99.4 0.11 5.4 6.6 63001
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) 2.5 2.59 97.3 0.616 6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.5 50 62929 3187 0.217 0.214 0.2177 0.259 0.2575 RANDOM 26.63
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] -0.28 -0.19 0.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.752 r_dihedral_angle_4_deg 19.237 r_dihedral_angle_3_deg 16.051 r_dihedral_angle_1_deg 5.244 r_scangle_it 2.157 r_scbond_it 1.324 r_angle_refined_deg 1.278 r_angle_other_deg 1.009 r_mcangle_it 0.845 r_symmetry_vdw_refined 0.446
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.752 r_dihedral_angle_4_deg 19.237 r_dihedral_angle_3_deg 16.051 r_dihedral_angle_1_deg 5.244 r_scangle_it 2.157 r_scbond_it 1.324 r_angle_refined_deg 1.278 r_angle_other_deg 1.009 r_mcangle_it 0.845 r_symmetry_vdw_refined 0.446 r_mcbond_it 0.436 r_symmetry_hbond_refined 0.254 r_symmetry_vdw_other 0.234 r_chiral_restr 0.158 r_xyhbond_nbd_refined 0.156 r_mcbond_other 0.142 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_gen_planes_other 0.006 r_bond_other_d 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10589 Nucleic Acid Atoms Solvent Atoms 189 Heterogen Atoms 164
Software Software Software Name Purpose MOLREP phasing REFMAC refinement