☰ Navigation Tabs
Crystal structure of the Vps10p domain of human sortilin/NTS3 in complex with Triazolone 1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3F6K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.3 292 0.1M HEPES-Tris pH=7.3
0.4 M Sodium malonate
22 % (w/V) PEG 3350
8 (V/V) glycerol
Crystal Properties Matthews coefficient Solvent content 3.6 65.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 162.395 α = 90 b = 78.23 β = 127.2 c = 111.796 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 CCD MARMOSAIC 225 mm CCD 2013-02-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-3 1.000 MAX II I911-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 2.5 66.9 98.7 0.063 0.998 11.4 3.4 38075 71
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.6 98.9 0.956 0.682 1.2 3.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3F6K 2.5 40.133 1.35 38072 1903 98.11 0.2121 0.211 0.213 0.2331 0.2348
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 17.039 f_angle_d 0.936 f_chiral_restr 0.057 f_plane_restr 0.008 f_bond_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5023 Nucleic Acid Atoms Solvent Atoms 57 Heterogen Atoms 77
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing