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The crystal structure of PDE2A complexed with inhibitor 13j
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4HTZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 289 0.1 M Tris-HCl (pH 8.5), 0.2 M MgCl2, and 18-22% PEG 3,350
Crystal Properties Matthews coefficient Solvent content 2.2 44.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.782 α = 109.62 b = 73.08 β = 91.183 c = 91.114 γ = 90.854
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 RIGAKU HyPix-3000 2022-10-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.5 23.732 98.6 0.088 13.1 3.8 46204 28.5081320208
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 2.5 2.6 99.3 0.339
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT NONE 2.50183917707 23.7317870663 1.99863227033 46093 2458 98.6579623288 0.259100558245 0.256210373668 0.2643 0.310908968797 0.3158 33.0741399015
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 18.0357067172 f_angle_d 0.504641540436 f_chiral_restr 0.0366298776666 f_plane_restr 0.00359062386825 f_bond_d 0.00271412917
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9920 Nucleic Acid Atoms Solvent Atoms 94 Heterogen Atoms 112
Software Software Software Name Purpose REFMAC refinement PHENIX refinement CrysalisPro data reduction Aimless data scaling PHASER phasing