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Crystal Structure of BACE1 in complex with N-{3-[(4S,6S)-2-amino-4-methyl-6-(trifluoromethyl)-5,6-dihydro-4H-1,3-thiazin-4-yl]-4-fluorophenyl}-5-(fluoromethoxy)pyrazine-2-carboxamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1W50
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293.15 0.2 M sodium citrate tribasic pH 6.5, 0.2 M ammonium iodide, 20.5% w/v PEG 5000MME
Crystal Properties Matthews coefficient Solvent content 2.73 59.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.59 α = 90 b = 101.59 β = 90 c = 170.351 γ = 120
Symmetry Space Group P 61 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV++ 2015-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54178
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 2.2 56.78 99.9 0.09 0.096 0.033 0.998 7.8 8 27088
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.27 99.6 0.448 0.478 0.165 0.924 8.1
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 1W50 2.2 20 25639 1407 99.82 0.1972 0.1951 0.2015 0.2339 0.2382 RANDOM 31.602
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 r_dihedral_angle_2_deg 35.544 r_dihedral_angle_4_deg 14.744 r_dihedral_angle_3_deg 13.999 r_dihedral_angle_1_deg 6.747 r_angle_refined_deg 1.329 r_angle_other_deg 0.762 r_chiral_restr 0.253 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.544 r_dihedral_angle_4_deg 14.744 r_dihedral_angle_3_deg 13.999 r_dihedral_angle_1_deg 6.747 r_angle_refined_deg 1.329 r_angle_other_deg 0.762 r_chiral_restr 0.253 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2862 Nucleic Acid Atoms Solvent Atoms 204 Heterogen Atoms 46
Software Software Software Name Purpose Aimless data extraction MOSFLM data processing MOLREP phasing REFMAC refinement