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Dimer structure of Sortilin ectodomain crystal form 3, 4.0 Angstrom
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5NMT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.2 291 0.18 M Magnesium formate dihydrate pH 7.0, 18% PEG 3350 (w/v), 1 mM CaCl2 and 1 mM GSH (L-Glutathione reduced) & GSSG (L-Glutathione oxidized), final pH 6.2
Crystal Properties Matthews coefficient Solvent content 2.85 56.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 150.32 α = 90 b = 151.82 β = 90 c = 162.74 γ = 90
Symmetry Space Group P 21 21 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-F 2014-02-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.97599 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 4 71.72 100 0.03936 0.05567 0.03936 0.998 7.7 12 32164
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 4 4.143 99.71 0.4076 0.5765 0.4076 0.789 1.83 2
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 5NMT 4 71.719 1.34 32054 1433 99.79 0.1892 0.1863 0.1888 0.2497 0.2504
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 12.767 f_angle_d 1.281 f_chiral_restr 0.071 f_bond_d 0.014 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20362 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 368
Software Software Software Name Purpose PHENIX refinement iMOSFLM data reduction Aimless data scaling PHASER phasing