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The crystal structure of PDE6D in complex to inhibitor-8
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3T5G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 0.1 M NaOAc, pH 4.6, 30 % PEG 4000, 0.2 M (NH4)2SO4
Crystal Properties Matthews coefficient Solvent content 3.05 59.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.76 α = 90 b = 55.76 β = 90 c = 114.92 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 IMAGE PLATE MAR scanner 345 mm plate 2015-05-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE ENRAF-NONIUS FR571 1.54179
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 1.87 27.88 99.6 0.091 15.6 8.2 16799
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 1.87 1.9 94.5 0.34 5.2 6.2
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 3T5G 1.87 27.88 16799 885 99.69 0.2053 0.2034 0.2124 0.2421 0.2487 RANDOM 26.384
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] 0.53 0.53 0.53 -1.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.127 r_dihedral_angle_4_deg 13.874 r_dihedral_angle_3_deg 12.854 r_dihedral_angle_1_deg 5.88 r_angle_refined_deg 1.354 r_angle_other_deg 1.014 r_chiral_restr 0.077 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.127 r_dihedral_angle_4_deg 13.874 r_dihedral_angle_3_deg 12.854 r_dihedral_angle_1_deg 5.88 r_angle_refined_deg 1.354 r_angle_other_deg 1.014 r_chiral_restr 0.077 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1178 Nucleic Acid Atoms Solvent Atoms 99 Heterogen Atoms 45
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction MOLREP phasing