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Structure of the cholesterol and lutein-binding domain of human STARD3 at 1.74A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EM2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9.1 295 0.85 M sodium/potassium tartrate, 0.2 M lithium sulfate, 0.1 M CHES, 0.01 M dithiothreitol. Cryostabilizer: 18% ethylene glycol, 5% ethanol in addition to 0.8M sodium/potassium tartrate, 0.1 M CHES pH 9.1, 0.2 M lithium sulfate, 0.01 M dithiothreitol. Crystals were frozen in propane and stored under liquid nitrogen
Crystal Properties Matthews coefficient Solvent content 3.2 61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.39 α = 90 b = 83.39 β = 90 c = 82.19 γ = 120
Symmetry Space Group P 31 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 ADSC QUANTUM 315r 2015-09-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 12.3.1 1.11583 ALS 12.3.1
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 1.74 37.18 99.5 0.046 0.999 25.8 8.8 34160 -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 1.74 1.79 98.6 0.81 2.4 6.8
Refinement Statistics Diffraction ID Structure Solution 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 1em2 1.74 37.18 1.34 34159 1712 99.54 0.17 0.1688 0.173 0.1919 0.1976 30.5
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 14.26 f_angle_d 1.161 f_chiral_restr 0.071 f_bond_d 0.013 f_plane_restr 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1695 Nucleic Acid Atoms Solvent Atoms 215 Heterogen Atoms 27
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling Coot model building PHASER phasing