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Structure of glycosylated NPC1 luminal domain C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.4 293 30% polyethylene glycol mono-ethyl Ether 2000 and 0.1 M potassium thiocyanate
Crystal Properties Matthews coefficient Solvent content 3.36 63.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.89 α = 90 b = 115.91 β = 90 c = 147.4 γ = 90
Symmetry Space Group C 2 2 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 2015-07-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 1.0675 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.45 70 100 13.3 26.5 28062
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 2.45 70.03 26647 1385 99.96 0.22474 0.22406 0.2258 0.23816 0.2375 RANDOM 73.014
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] 1.07 -2.19 1.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.245 r_dihedral_angle_3_deg 14.615 r_dihedral_angle_4_deg 13.237 r_long_range_B_refined 7.35 r_long_range_B_other 7.339 r_dihedral_angle_1_deg 6.22 r_scangle_other 4.17 r_mcangle_it 3.965 r_mcangle_other 3.964 r_scbond_it 2.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.245 r_dihedral_angle_3_deg 14.615 r_dihedral_angle_4_deg 13.237 r_long_range_B_refined 7.35 r_long_range_B_other 7.339 r_dihedral_angle_1_deg 6.22 r_scangle_other 4.17 r_mcangle_it 3.965 r_mcangle_other 3.964 r_scbond_it 2.39 r_scbond_other 2.387 r_mcbond_it 2.201 r_mcbond_other 2.192 r_angle_refined_deg 1.519 r_angle_other_deg 1.1 r_chiral_restr 0.083 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.003 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3499 Nucleic Acid Atoms Solvent Atoms 44 Heterogen Atoms 316
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Coot model building PHENIX phasing