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The crystal structure of PDE6D in complex to inhibitor-7
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 1.4 M NaOAc, 0.1 M NaCAC, pH 6.8
Crystal Properties Matthews coefficient Solvent content 3.02 59.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.95 α = 90 b = 55.95 β = 90 c = 115.3 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 2015-03-06 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 2.4 27.98 99.9 0.161 17.1 11 8200
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 2.4 2.5 99.9 0.85 3.6 11.1
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 2.4 27.98 8200 432 99.87 0.1886 0.1853 0.1894 0.254 0.2523 RANDOM 28.103
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] 0.48 0.48 0.48 -1.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.377 r_dihedral_angle_3_deg 13.812 r_dihedral_angle_4_deg 12.01 r_dihedral_angle_1_deg 6.463 r_angle_refined_deg 1.466 r_angle_other_deg 0.919 r_chiral_restr 0.094 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.377 r_dihedral_angle_3_deg 13.812 r_dihedral_angle_4_deg 12.01 r_dihedral_angle_1_deg 6.463 r_angle_refined_deg 1.466 r_angle_other_deg 0.919 r_chiral_restr 0.094 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1200 Nucleic Acid Atoms Solvent Atoms 63 Heterogen Atoms 46
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction MOLREP phasing