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Structure of Fully modified farnesylated INPP5E Peptide in complex with PDE6D
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, SITTING DROP 7.5 293 1.4 M sodium malonate
Crystal Properties Matthews coefficient Solvent content 2.58 52.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.47 α = 90 b = 81.2 β = 90 c = 117.21 γ = 90
Symmetry Space Group C 2 2 21
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 2013-12-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.007 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 1.85 19.53 99.8 0.097 10.42 6.39 30251
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 1.85 1.9 100 0.672 3.09 6.58
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 1.85 19.53 30251 1593 99.84 0.1736 0.1719 0.1802 0.2075 0.2122 RANDOM 35.377
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] -1.09 1.37 -0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.564 r_dihedral_angle_3_deg 13.632 r_dihedral_angle_4_deg 11.662 r_dihedral_angle_1_deg 6.51 r_mcangle_it 3.728 r_mcbond_it 2.98 r_mcbond_other 2.969 r_angle_refined_deg 2.011 r_angle_other_deg 0.854 r_chiral_restr 0.114
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.564 r_dihedral_angle_3_deg 13.632 r_dihedral_angle_4_deg 11.662 r_dihedral_angle_1_deg 6.51 r_mcangle_it 3.728 r_mcbond_it 2.98 r_mcbond_other 2.969 r_angle_refined_deg 2.011 r_angle_other_deg 0.854 r_chiral_restr 0.114 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2528 Nucleic Acid Atoms Solvent Atoms 89 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing Coot model building