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The crystal structure of PDE6D in complex to Deltasonamide1
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 0.2 M NaOAc, 0.1 M Na3Cit, pH 5.5, 10 % PEG 4000
Crystal Properties Matthews coefficient Solvent content 3.02 59.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.01 α = 90 b = 56.01 β = 90 c = 115.09 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 PILATUS3 6M 2014-12-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.978 SLS X10SA
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 1.4 44.7 100 0.075 16.5 9.6 39854
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 1.4 1.5 100 0.64 3.4 9.4
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 1.4 44.7 39854 2098 99.96 0.1898 0.1891 0.1978 0.2034 0.2086 RANDOM 20.788
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] 0.36 0.36 0.36 -1.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.26 r_dihedral_angle_4_deg 16.345 r_dihedral_angle_3_deg 11.861 r_dihedral_angle_1_deg 6.039 r_angle_refined_deg 1.665 r_angle_other_deg 0.998 r_chiral_restr 0.127 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.26 r_dihedral_angle_4_deg 16.345 r_dihedral_angle_3_deg 11.861 r_dihedral_angle_1_deg 6.039 r_angle_refined_deg 1.665 r_angle_other_deg 0.998 r_chiral_restr 0.127 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1193 Nucleic Acid Atoms Solvent Atoms 180 Heterogen Atoms 43
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction MOLREP phasing