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Crystal structure of the human BACE1 catalytic domain in complex with N-(1-benzyl-piperidin-4-yl)-4-mercapto-butyramide
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 6.5 295 0.1M Bis-Tris pH 6.5, 0.1M sodium chloride, 1.5M ammonium sulfate, 7.0 mg/ml Beta-secretase 1 , VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.89 57.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.596 α = 90 b = 103.596 β = 90 c = 168.741 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 2004-02-10 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 2.6 20 99 0.111 10.8 17118 16879
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) 1 2.6 2.69 0.432
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 PDB ENTRY 2P8H 2.6 20 15848 844 97.84 0.22893 0.22684 0.226 0.26859 0.2678 RANDOM 38.902
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] -0.38 -0.19 -0.38 0.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.136 r_dihedral_angle_4_deg 17.615 r_dihedral_angle_3_deg 15.351 r_dihedral_angle_1_deg 5.705 r_mcangle_it 3.196 r_scangle_it 2.352 r_mcbond_it 1.896 r_scbond_it 1.519 r_angle_refined_deg 0.964 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.136 r_dihedral_angle_4_deg 17.615 r_dihedral_angle_3_deg 15.351 r_dihedral_angle_1_deg 5.705 r_mcangle_it 3.196 r_scangle_it 2.352 r_mcbond_it 1.896 r_scbond_it 1.519 r_angle_refined_deg 0.964 r_nbtor_refined 0.305 r_nbd_refined 0.178 r_symmetry_vdw_refined 0.157 r_xyhbond_nbd_refined 0.125 r_symmetry_hbond_refined 0.064 r_chiral_restr 0.061 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 2771 Nucleic Acid Atoms Solvent Atoms 99 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection d*TREK data reduction d*TREK data scaling AMoRE phasing