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The crystal structure of PDE6D in complex to inhibitor-4
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 20 % PEG 3350, 0.2 M Na2SO4
Crystal Properties Matthews coefficient Solvent content 3.14 60.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.15 α = 90 b = 56.15 β = 90 c = 115.15 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 2014-07-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.0 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 2.6 28.07 99.9 0.14 20.04 19 6541
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 2.6 2.7 100 0.76 4.8 20.3
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 2.6 28.07 6541 345 99.88 0.2064 0.2039 0.2051 0.2514 0.2408 RANDOM 40.678
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] 0.86 0.86 0.86 -2.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.292 r_dihedral_angle_3_deg 14.709 r_dihedral_angle_4_deg 12.893 r_dihedral_angle_1_deg 6.449 r_angle_refined_deg 1.389 r_angle_other_deg 1.034 r_chiral_restr 0.084 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 41.292 r_dihedral_angle_3_deg 14.709 r_dihedral_angle_4_deg 12.893 r_dihedral_angle_1_deg 6.449 r_angle_refined_deg 1.389 r_angle_other_deg 1.034 r_chiral_restr 0.084 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 1168 Nucleic Acid Atoms Solvent Atoms 22 Heterogen Atoms 41
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction MOLREP phasing