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Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-3098
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3SL3
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 2.65 53.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.99 α = 90 b = 110.76 β = 90 c = 161.34 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 2017-09-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97625 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 2.34 80.67 100 0.134 0.146 0.057 0.997 10.3 6.6 75517
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 2.34 2.4 100 1.283 1.391 0.534 0.564 1.5 6.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 3SL3 2.34 80.67 71654 3788 99.96 0.18419 0.18122 0.1907 0.24012 0.2453 RANDOM 52.888
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] 1.18 -0.4 -0.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.705 r_dihedral_angle_4_deg 17.889 r_dihedral_angle_3_deg 16.697 r_long_range_B_refined 9.227 r_long_range_B_other 9.227 r_scangle_other 7.452 r_dihedral_angle_1_deg 5.937 r_mcangle_it 5.487 r_mcangle_other 5.487 r_scbond_it 4.958
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.705 r_dihedral_angle_4_deg 17.889 r_dihedral_angle_3_deg 16.697 r_long_range_B_refined 9.227 r_long_range_B_other 9.227 r_scangle_other 7.452 r_dihedral_angle_1_deg 5.937 r_mcangle_it 5.487 r_mcangle_other 5.487 r_scbond_it 4.958 r_scbond_other 4.953 r_mcbond_it 3.818 r_mcbond_other 3.818 r_angle_refined_deg 1.735 r_angle_other_deg 1.045 r_chiral_restr 0.117 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 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 484 Heterogen Atoms 401
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing