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Crystal structure of human phosphodiesterase 4B (PDE4B) in complex with a [1,3,5]triazine derivative
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.9 293 ethylene glycole, PEG1K, pH 5.9, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.09 41.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.332 α = 90 b = 53.332 β = 90 c = 229.048 γ = 90
Symmetry Space Group P 43 21 2
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 MARRESEARCH Rh coated meridionally focussing mirror 2005-07-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.9793 SLS X06SA
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 1.5 57.26 89.3 0.082 4.7 3.8 48537 48537
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 89.3
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 1.5 57.26 48537 47008 1529 89.25 0.16872 0.1678 0.1753 0.19763 0.2055 RANDOM 19.856
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] 0.47 0.47 -0.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.677 r_dihedral_angle_4_deg 15.36 r_dihedral_angle_3_deg 11.602 r_scangle_it 5.726 r_dihedral_angle_1_deg 5.03 r_scbond_it 3.808 r_mcangle_it 2.382 r_mcbond_it 1.481 r_angle_refined_deg 1.359 r_angle_other_deg 1.283
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.677 r_dihedral_angle_4_deg 15.36 r_dihedral_angle_3_deg 11.602 r_scangle_it 5.726 r_dihedral_angle_1_deg 5.03 r_scbond_it 3.808 r_mcangle_it 2.382 r_mcbond_it 1.481 r_angle_refined_deg 1.359 r_angle_other_deg 1.283 r_mcbond_other 0.491 r_symmetry_hbond_refined 0.363 r_symmetry_vdw_other 0.267 r_symmetry_vdw_refined 0.189 r_xyhbond_nbd_refined 0.157 r_chiral_restr 0.077 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2621 Nucleic Acid Atoms Solvent Atoms 151 Heterogen Atoms 99
Software Software Software Name Purpose MAR345 data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling