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Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-637
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 pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.63 53.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.108 α = 90 b = 110.311 β = 90 c = 160.722 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 PILATUS 6M-F 2018-03-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91587 Diamond I04-1
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 2 90.93 100 0.118 0.129 0.05 0.996 8.5 6.5 119392
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 2 2.05 99.9 0.763 0.829 0.321 0.564 2.1 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 2 84.5 111310 5902 98.11 0.20227 0.19994 0.21 0.24614 0.2501 RANDOM 35.584
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] -0.6 -0.23 0.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.901 r_dihedral_angle_4_deg 18.088 r_dihedral_angle_3_deg 15.654 r_long_range_B_refined 7.25 r_long_range_B_other 7.25 r_dihedral_angle_1_deg 6.044 r_scangle_other 5.494 r_mcangle_it 3.823 r_mcangle_other 3.822 r_scbond_it 3.706
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.901 r_dihedral_angle_4_deg 18.088 r_dihedral_angle_3_deg 15.654 r_long_range_B_refined 7.25 r_long_range_B_other 7.25 r_dihedral_angle_1_deg 6.044 r_scangle_other 5.494 r_mcangle_it 3.823 r_mcangle_other 3.822 r_scbond_it 3.706 r_scbond_other 3.706 r_mcbond_it 2.762 r_mcbond_other 2.761 r_angle_refined_deg 1.621 r_angle_other_deg 1.357 r_chiral_restr 0.118 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 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_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 655 Heterogen Atoms 354
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling REFMAC phasing