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Crystal structure of the catalytic domain of human PDE3A bound to AMP
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 44.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.415 α = 90 b = 58.783 β = 90.74 c = 156.996 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 2018-08-31 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) R Merge I (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 2.08 47.9 99.5 0.074 0.087 0.998 12.2 3.653 90479 46.236
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.08 2.2 99 0.982 1.15 0.581 1.82 3.623
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT ISO2 2.08 47.9 86225 4207 99.52 0.2357 0.2348 0.253 0.2485 RANDOM 74.491
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] -0.08 -0.45 -0.06 0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.999 r_dihedral_angle_4_deg 16.83 r_dihedral_angle_3_deg 13.807 r_dihedral_angle_1_deg 5.155 r_angle_other_deg 2.323 r_angle_refined_deg 1.82 r_chiral_restr 0.152 r_bond_other_d 0.035 r_bond_refined_d 0.016 r_gen_planes_other 0.009
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.999 r_dihedral_angle_4_deg 16.83 r_dihedral_angle_3_deg 13.807 r_dihedral_angle_1_deg 5.155 r_angle_other_deg 2.323 r_angle_refined_deg 1.82 r_chiral_restr 0.152 r_bond_other_d 0.035 r_bond_refined_d 0.016 r_gen_planes_other 0.009 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11915 Nucleic Acid Atoms Solvent Atoms 273 Heterogen Atoms 88
Software Software Software Name Purpose XDS data reduction XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction PHENIX phasing