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Crystal structure of the catalytic domain of human PDE3A bound to DNMDP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SO2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.9 293.15 MES, PEG 3350, calcium acetate
Crystal Properties Matthews coefficient Solvent content 2.2 44.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.21 α = 90 b = 58.52 β = 90.66 c = 157.54 γ = 90
Symmetry Space Group P 1 21 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 S 6M 2018-06-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.976251 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 47.7 94.3 0.057 0.998 10.79 1.8 187181
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.11 91.7 0.747 0.64 1.47 1.7
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 1SO2 2 47.7 95542 5030 99.22 0.1864 0.1846 0.195 0.2192 0.2263 RANDOM 49.716
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] 0.5 0.34 0.53 -1.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.455 r_dihedral_angle_3_deg 15.089 r_dihedral_angle_4_deg 13.951 r_dihedral_angle_1_deg 6.494 r_angle_refined_deg 1.732 r_angle_other_deg 1.426 r_chiral_restr 0.093 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.455 r_dihedral_angle_3_deg 15.089 r_dihedral_angle_4_deg 13.951 r_dihedral_angle_1_deg 6.494 r_angle_refined_deg 1.732 r_angle_other_deg 1.426 r_chiral_restr 0.093 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11926 Nucleic Acid Atoms Solvent Atoms 359 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XDS data scaling PHENIX phasing