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Crystal structure of the human BACE1 catalytic domain in complex with 4-(4-fluoro-benzyl)-piperazine-2-carboxylic acid(3-mercapto-propyl)-amide
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 5.5 295 0.1M Bis-Tris pH 5.5, 0.2M lithium sulfate monohydrate, 25% w/v polyethylene glycol 3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.91 57.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 233.149 α = 90 b = 108.546 β = 103.34 c = 64.091 γ = 90
Symmetry Space Group C 1 2 1
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 2004-02-24 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 2.8 20 0.104 101873 37401
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) 2.8 2.9 0.555
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 3 20 28202 1471 95.32 0.249 0.24676 0.2373 0.29316 0.2783 RANDOM 65.905
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] -6.6 -0.7 -1.28 7.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.99 r_dihedral_angle_4_deg 16.162 r_dihedral_angle_3_deg 15.243 r_dihedral_angle_1_deg 4.96 r_mcangle_it 2.322 r_scangle_it 1.511 r_mcbond_it 1.34 r_scbond_it 0.917 r_angle_refined_deg 0.916 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.99 r_dihedral_angle_4_deg 16.162 r_dihedral_angle_3_deg 15.243 r_dihedral_angle_1_deg 4.96 r_mcangle_it 2.322 r_scangle_it 1.511 r_mcbond_it 1.34 r_scbond_it 0.917 r_angle_refined_deg 0.916 r_nbtor_refined 0.303 r_symmetry_hbond_refined 0.216 r_nbd_refined 0.17 r_symmetry_vdw_refined 0.159 r_xyhbond_nbd_refined 0.116 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 8634 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 63
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection d*TREK data reduction d*TREK data scaling AMoRE phasing