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Crystal structure of human phosphodiesterase 4d with d155871
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 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 52.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.865 α = 90 b = 113.241 β = 90 c = 161.22 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 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.97 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 1.9 50 92.9 0.057 8.9 3.8 132652
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) 1.9 1.97 93.3 0.581 2.9
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.9 50 132466 6596 0.183 0.181 0.215 0.2038 RANDOM 20.39
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] 0.73 -0.86 0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.127 r_dihedral_angle_4_deg 16.616 r_dihedral_angle_3_deg 13.623 r_dihedral_angle_1_deg 4.984 r_scangle_it 2.609 r_scbond_it 1.786 r_angle_refined_deg 1.157 r_mcangle_it 1.093 r_angle_other_deg 0.945 r_mcbond_it 0.789
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.127 r_dihedral_angle_4_deg 16.616 r_dihedral_angle_3_deg 13.623 r_dihedral_angle_1_deg 4.984 r_scangle_it 2.609 r_scbond_it 1.786 r_angle_refined_deg 1.157 r_mcangle_it 1.093 r_angle_other_deg 0.945 r_mcbond_it 0.789 r_symmetry_vdw_other 0.253 r_symmetry_vdw_refined 0.231 r_nbd_refined 0.215 r_xyhbond_nbd_refined 0.195 r_symmetry_hbond_refined 0.188 r_nbd_other 0.183 r_nbtor_refined 0.17 r_mcbond_other 0.155 r_nbtor_other 0.083 r_chiral_restr 0.066 r_metal_ion_refined 0.015 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other 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 10655 Nucleic Acid Atoms Solvent Atoms 1203 Heterogen Atoms 159
Software Software Software Name Purpose MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling