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Crystal structure of the Vps10p domain of human sortilin/NTS3 in complex with AF38469
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3F6K PDB ENTRY 3F6K with ligand, glycosylations and waters removed
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.3 292 0.1 M HEPES-Tris, 0.4 M sodium malonate, 27 % (w/v) PEG 3350, 4.5 % (v/v) glycerol, pH 7.3, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 3.57 65.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 161.948 α = 90 b = 77.402 β = 127.06 c = 111.176 γ = 90
Symmetry Space Group C 1 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 2M-F 2012-05-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 0.9000 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.7 46.7 99.7 0.071 0.071 15.2 6.9 30397 30397 1.34 2 84.3
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 2.7 2.8 97.9 0.845 2.2
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 PDB ENTRY 3F6K with ligand, glycosylations and waters removed 2.7 44.4 1.34 30397 30366 2223 99.6 0.2038 0.2008 0.2044 0.2416 0.2423 Random
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.237 f_angle_d 1.354 f_chiral_restr 0.061 f_bond_d 0.011 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5140 Nucleic Acid Atoms Solvent Atoms 51 Heterogen Atoms 100
Software Software Software Name Purpose DNA data collection PHASER phasing PHENIX refinement XDS data reduction SCALA data scaling