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Crystal structure of human phosphodiesterase 4D with bound allosteric modulator
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 100MM HEPES, 35% ETHYLENE GLYCOL, 5% GLYCEROL, 22% PEG 3350, pH 7.50, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.55 51.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.551 α = 90 b = 111.997 β = 90 c = 162.384 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 CCD ADSC QUANTUM 210 2007-02-05 M 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 2.65 92.06 93.2 0.192 4.1 5.2 48999
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) 2.65 2.74 95.2 0.803 4.8
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 2.65 50 48955 2479 0.217 0.214 0.2137 0.267 0.2627 RANDOM 18.23
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] 0.21 -0.38 0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.539 r_dihedral_angle_4_deg 15.33 r_dihedral_angle_3_deg 15.254 r_dihedral_angle_1_deg 4.723 r_scangle_it 1.286 r_angle_refined_deg 0.984 r_angle_other_deg 0.901 r_scbond_it 0.748 r_mcangle_it 0.583 r_mcbond_it 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.539 r_dihedral_angle_4_deg 15.33 r_dihedral_angle_3_deg 15.254 r_dihedral_angle_1_deg 4.723 r_scangle_it 1.286 r_angle_refined_deg 0.984 r_angle_other_deg 0.901 r_scbond_it 0.748 r_mcangle_it 0.583 r_mcbond_it 0.301 r_chiral_restr 0.049 r_mcbond_other 0.036 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10951 Nucleic Acid Atoms Solvent Atoms 203 Heterogen Atoms 243
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling