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The crystal structure of PDE6D in complex with inhibitor-3
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 30 % PEG 4000, 0.2 M NaOAc, 0.1 M TRIS-HCL, pH 8.5
Crystal Properties Matthews coefficient Solvent content 3.08 60.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.65 α = 90 b = 55.65 β = 90 c = 115.34 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 PILATUS 6M 2012-09-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.97889 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 1.6 27.83 99.9 0.063 28.8 19.1 26598
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 1.6 1.7 99.8 0.44 7.5 19.3
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 1.6 27.83 26598 1400 99.86 0.2035 0.2023 0.2087 0.2274 0.2365 RANDOM 23.874
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] 0.5 0.5 0.5 -1.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.296 r_dihedral_angle_4_deg 15.839 r_dihedral_angle_3_deg 10.422 r_dihedral_angle_1_deg 6.098 r_angle_refined_deg 1.554 r_angle_other_deg 0.853 r_chiral_restr 0.113 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.296 r_dihedral_angle_4_deg 15.839 r_dihedral_angle_3_deg 10.422 r_dihedral_angle_1_deg 6.098 r_angle_refined_deg 1.554 r_angle_other_deg 0.853 r_chiral_restr 0.113 r_bond_refined_d 0.011 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 1173 Nucleic Acid Atoms Solvent Atoms 131 Heterogen Atoms 34
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction MOLREP phasing