☰ Navigation Tabs
Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-1439
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 24% PEG 3350, 30% Ethylene Glycol, 0.1 M HEPES
Crystal Properties Matthews coefficient Solvent content 2.6 52.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.19 α = 90 b = 110.71 β = 90 c = 161.48 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 PIXEL DECTRIS PILATUS3 6M CRL 2017-02-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97624 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.88 55.35 100 0.085 0.092 0.035 0.999 13.7 6.7 141825
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.88 1.93 100 1.727 1.875 0.726 0.498 1.2 6.6
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 FOURIER SYNTHESIS THROUGHOUT 1.88 55.35 134495 7234 99.92 0.17291 0.17148 0.1841 0.19932 0.21 RANDOM 40.058
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] -0.1 -1.89 1.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.927 r_dihedral_angle_4_deg 19.254 r_dihedral_angle_3_deg 13.597 r_long_range_B_refined 8.128 r_long_range_B_other 8.128 r_scangle_other 7.006 r_scbond_it 5.126 r_scbond_other 5.126 r_dihedral_angle_1_deg 5.073 r_mcangle_it 4.344
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.927 r_dihedral_angle_4_deg 19.254 r_dihedral_angle_3_deg 13.597 r_long_range_B_refined 8.128 r_long_range_B_other 8.128 r_scangle_other 7.006 r_scbond_it 5.126 r_scbond_other 5.126 r_dihedral_angle_1_deg 5.073 r_mcangle_it 4.344 r_mcangle_other 4.344 r_mcbond_it 3.466 r_mcbond_other 3.466 r_angle_refined_deg 1.881 r_angle_other_deg 1.088 r_chiral_restr 0.112 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 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_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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10515 Nucleic Acid Atoms Solvent Atoms 625 Heterogen Atoms 583
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing