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BACE2 xaperone complex with N-{3-[(5R)-3-amino-5-methyl-9,9-dioxo-2,9lambda6-dithia-4-azaspiro[5.5]undec-3-en-5-yl]-4-fluorophenyl}-5-(fluoromethoxy)pyrazine-2-carboxamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ZKG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293.15 0.1M TRIS pH 8.0, 25% PEG 3350, pH 8.0
Crystal Properties Matthews coefficient Solvent content 2.31 46.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.542 α = 90 b = 74.467 β = 90 c = 109.135 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 EIGER X 16M 2016-06-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.0000 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) 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 1.53 61.51 99.5 0.035 0.04 19.09 4.1 78375
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.53 1.78 99.1 0.49 0.563 4.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT 3ZKG 1.53 61.51 74276 4099 99.67 0.2258 0.2252 0.2311 0.237 0.2411 RANDOM 28.96
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] -0.45 -1.8 2.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.944 r_dihedral_angle_4_deg 12.371 r_dihedral_angle_3_deg 11.01 r_dihedral_angle_1_deg 5.859 r_angle_refined_deg 1.439 r_angle_other_deg 1.187 r_chiral_restr 0.079 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.944 r_dihedral_angle_4_deg 12.371 r_dihedral_angle_3_deg 11.01 r_dihedral_angle_1_deg 5.859 r_angle_refined_deg 1.439 r_angle_other_deg 1.187 r_chiral_restr 0.079 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3560 Nucleic Acid Atoms Solvent Atoms 299 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing