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Crystal structure of the human BACE1 catalytic domain in complex with N-[1-(5-bromo-2,3-dimethoxy-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 sodium cacodylate pH 6.5, 1.26M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.9 57.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.091 α = 90 b = 104.091 β = 90 c = 167.98 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 CCD ADSC QUANTUM 315 2004-04-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 1.08 SSRL BL7-1
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 2.1 20 98.4 0.065 31523
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) 2.1 2.17 0.339
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 2.1 20 29497 1583 97.02 0.25951 0.25786 0.29051 0.2815 RANDOM 39.157
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 34.102 r_dihedral_angle_4_deg 13.368 r_dihedral_angle_3_deg 13.155 r_dihedral_angle_1_deg 5.384 r_mcangle_it 2.697 r_scangle_it 1.977 r_mcbond_it 1.622 r_scbond_it 1.283 r_angle_refined_deg 0.946 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.102 r_dihedral_angle_4_deg 13.368 r_dihedral_angle_3_deg 13.155 r_dihedral_angle_1_deg 5.384 r_mcangle_it 2.697 r_scangle_it 1.977 r_mcbond_it 1.622 r_scbond_it 1.283 r_angle_refined_deg 0.946 r_nbtor_refined 0.305 r_nbd_refined 0.164 r_symmetry_vdw_refined 0.161 r_xyhbond_nbd_refined 0.112 r_symmetry_hbond_refined 0.081 r_chiral_restr 0.057 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 2668 Nucleic Acid Atoms Solvent Atoms 271 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection d*TREK data reduction d*TREK data scaling AMoRE phasing