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The crystal structure of PDE5 with 1934
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2H42
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 0.2 M MgSO4, 0.1 M Cacodylate sodium salt, pH 6.5, 2.5% ethanol, and 18% PEG3350
Crystal Properties Matthews coefficient Solvent content 1.01 21.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.75 α = 90 b = 73.75 β = 90 c = 128.64 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 RIGAKU HyPix-3000 2021-01-06 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 24.24 99.96 0.088 19.7 8.5 14545
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 2.6 100 0.867 2.1 8.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 2H42 2.50007004666 24.2372400269 1.3612763452 14543 713 99.9450209608 0.216232731989 0.213580007315 0.2197 0.271068440537 0.2806 53.8208699243
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 16.4179594726 f_angle_d 1.0121554334 f_chiral_restr 0.0532955220353 f_bond_d 0.00898900909993 f_plane_restr 0.00644282696048
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2360 Nucleic Acid Atoms Solvent Atoms 48 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement PHENIX refinement CrysalisPro data reduction