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Crystal structure of BACE1 in complex with hydroxyethylamine inhibitor 37
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DUY PDB ENTRY 3DUY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 293 16% polyethylene glycol 8000, 0.1 M sodium citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.11 60.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.704 α = 90 b = 104.765 β = 103.87 c = 101.557 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315r 2011-05-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.0000 ALS 5.0.2
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 50 100 0.067 12.9 3.8 113395 113395 -3
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 2.07 100 0.546 3.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 3DUY 2 49.33 113412 107626 5714 99.94 0.19657 0.19482 0.1915 0.22948 0.2219 RANDOM 47.52
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] -0.77 0.17 0.96 -0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.92 r_dihedral_angle_4_deg 14.981 r_dihedral_angle_3_deg 12.541 r_dihedral_angle_1_deg 6.019 r_scangle_it 1.954 r_mcangle_it 1.609 r_scbond_it 1.266 r_angle_refined_deg 1.125 r_mcbond_it 0.966 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.92 r_dihedral_angle_4_deg 14.981 r_dihedral_angle_3_deg 12.541 r_dihedral_angle_1_deg 6.019 r_scangle_it 1.954 r_mcangle_it 1.609 r_scbond_it 1.266 r_angle_refined_deg 1.125 r_mcbond_it 0.966 r_nbtor_refined 0.306 r_symmetry_vdw_refined 0.199 r_nbd_refined 0.178 r_symmetry_hbond_refined 0.156 r_xyhbond_nbd_refined 0.111 r_chiral_restr 0.071 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 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 8826 Nucleic Acid Atoms Solvent Atoms 952 Heterogen Atoms 156
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing