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Crystal structure of human phosphodiesterase 4B catalytic domain with inhibitor NPD-001
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3G45
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 293 50 mM calcium acetate, 20% PEG 400, 100 mM sodium acetate
Crystal Properties Matthews coefficient Solvent content 2.35 47.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.737 α = 90 b = 95.737 β = 90 c = 85.113 γ = 120
Symmetry Space Group P 31 2 1
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 2016-04-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97623 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.4 82.91 100 0.129 0.998 13 8.5 17941
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) 1 2.4 2.53 100 0.78 2.3 6.1
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 3G45 2.4 82.91 17166 744 99.94 0.17408 0.17113 0.1805 0.24084 0.2467 RANDOM 51.062
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] 1.03 0.51 1.03 -3.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.611 r_dihedral_angle_4_deg 24.417 r_dihedral_angle_3_deg 15.509 r_long_range_B_refined 8.679 r_long_range_B_other 8.678 r_scangle_other 7.065 r_dihedral_angle_1_deg 5.914 r_mcangle_it 5.243 r_mcangle_other 5.243 r_scbond_it 4.552
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.611 r_dihedral_angle_4_deg 24.417 r_dihedral_angle_3_deg 15.509 r_long_range_B_refined 8.679 r_long_range_B_other 8.678 r_scangle_other 7.065 r_dihedral_angle_1_deg 5.914 r_mcangle_it 5.243 r_mcangle_other 5.243 r_scbond_it 4.552 r_scbond_other 4.551 r_mcbond_it 3.589 r_mcbond_other 3.566 r_angle_refined_deg 1.582 r_angle_other_deg 1 r_chiral_restr 0.088 r_bond_refined_d 0.013 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 2720 Nucleic Acid Atoms Solvent Atoms 85 Heterogen Atoms 57
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing