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Crystal structure of the human BACE1 catalytic domain in complex with N-[1-(5-chloro-2-isopropoxy-3-methoxy-benzyl)-piperidin-4-yl]-2-(2-methyl-4-sulfamoyl-phenoxy)-acetamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2P8H PDB ENTRY 2P8H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 295 6mg/ml BACE1, 0.1M HEPES pH 7.5, 1.5M Li2SO4, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.88 57.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.989 α = 90 b = 103.989 β = 90 c = 167.081 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 180 IMAGE PLATE RIGAKU RAXIS IV 2005-01-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.7 20 99.7 0.097 15302 15191
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) 2.7 2.8 0.328
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2P8H 2.7 20 14385 748 99.28 0.22395 0.22212 0.25977 0.2254 RANDOM 38.158
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] -0.75 -0.37 -0.75 1.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.89 r_dihedral_angle_3_deg 14.345 r_dihedral_angle_4_deg 12.543 r_dihedral_angle_1_deg 4.807 r_mcangle_it 2.152 r_scangle_it 1.549 r_mcbond_it 1.241 r_scbond_it 0.938 r_angle_refined_deg 0.881 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.89 r_dihedral_angle_3_deg 14.345 r_dihedral_angle_4_deg 12.543 r_dihedral_angle_1_deg 4.807 r_mcangle_it 2.152 r_scangle_it 1.549 r_mcbond_it 1.241 r_scbond_it 0.938 r_angle_refined_deg 0.881 r_nbtor_refined 0.302 r_nbd_refined 0.163 r_symmetry_vdw_refined 0.136 r_xyhbond_nbd_refined 0.104 r_symmetry_hbond_refined 0.104 r_chiral_restr 0.055 r_bond_refined_d 0.006 r_gen_planes_refined 0.002 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2878 Nucleic Acid Atoms Solvent Atoms 52 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection d*TREK data reduction d*TREK data scaling AMoRE phasing