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Crystal structure of S. cerevisia Niemann-Pick type C protein NPC2 with ergosterol bound
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4 292 Lithium Sulfate Monohydrate, Sodium Acetate Trihydrate, PEG 200
Crystal Properties Matthews coefficient Solvent content 5.9 79.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 215.39 α = 90 b = 215.39 β = 90 c = 129.81 γ = 120
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 2017-12-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.96864 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 2.9 47.751 100 0.326 0.341 0.993 8.08 11.6 75858 65.84
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 3 99.9 3.102 3.246 0.279 0.85 11.564
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SIRAS THROUGHOUT 2.9 47.751 1.35 75826 1990 99.94 0.2266 0.2258 0.2285 0.2567 0.2584 69.6773
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 12.119 f_angle_d 1.423 f_chiral_restr 0.09 f_bond_d 0.011 f_plane_restr 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10121 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 365
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling MLPHARE phasing PDB_EXTRACT data extraction