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Crystal structure of covalent PDE6delta adduct modified by compound 13b
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5ML8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 0.1 M NaOAc, pH = 4.71, 5.6% w/v PEG4000, 30% v/v glycerol
Crystal Properties Matthews coefficient Solvent content 2.37 48.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.65 α = 90 b = 55.65 β = 90 c = 115.84 γ = 120
Symmetry Space Group P 32 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 EIGER2 X 9M 2023-09-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 1.00 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 1.8 48.19 100 0.096 0.099 1 17.71 19.56 19921
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 1.8 1.85 2.127 2.188 0.777
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 FREE R-VALUE 1.8 48.19 1.36 19875 996 99.74 0.2064 0.2052 0.2057 0.2279 0.2291
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 18.19 f_angle_d 0.698 f_chiral_restr 0.046 f_plane_restr 0.007 f_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1205 Nucleic Acid Atoms Solvent Atoms 78 Heterogen Atoms 50
Software Software Software Name Purpose PHENIX refinement XSCALE data scaling XDS data reduction PDB_EXTRACT data extraction PHASER phasing