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Crystal structure of the Vps10p domain of human sortilin/NTS3 in complex with neurotensin
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.8 293 19% PEG 6000, 600 mM NaCl, 3% Glycerol, 100 mM HEPES, 93 mM Tris-HCl, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.79 55.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 145.76 α = 90 b = 74.53 β = 131.87 c = 108.33 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 2005-10-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.95008 SLS X06SA
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 2 50 96.9 0.073 11.59 3.6 58793 56985 -3 37.05
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 2.1 98.8 0.44 4.32 3.7 7942
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MIRAS THROUGHOUT 2 40.32 56985 56985 2904 97.39 0.20524 0.20524 0.20395 0.22879 0.2721 RANDOM 31.78
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] -0.58 -0.78 1.22 -1.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.684 r_dihedral_angle_4_deg 22.079 r_dihedral_angle_3_deg 16.77 r_dihedral_angle_1_deg 7.053 r_scangle_it 4.816 r_scbond_it 3.273 r_mcangle_it 2.29 r_angle_refined_deg 1.832 r_mcbond_it 1.446 r_nbtor_refined 0.319
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.684 r_dihedral_angle_4_deg 22.079 r_dihedral_angle_3_deg 16.77 r_dihedral_angle_1_deg 7.053 r_scangle_it 4.816 r_scbond_it 3.273 r_mcangle_it 2.29 r_angle_refined_deg 1.832 r_mcbond_it 1.446 r_nbtor_refined 0.319 r_xyhbond_nbd_refined 0.268 r_nbd_refined 0.238 r_symmetry_hbond_refined 0.235 r_symmetry_vdw_refined 0.223 r_chiral_restr 0.137 r_bond_refined_d 0.021 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5212 Nucleic Acid Atoms Solvent Atoms 305 Heterogen Atoms 83
Software Software Software Name Purpose XDS data scaling SHARP phasing REFMAC refinement XDS data reduction XSCALE data scaling