☰ Navigation Tabs
Crystal structure of the human BACE1 catalytic domain in complex with 4-(4-fluoro-benzyl)-piperazine-2-carboxylic acid (2-mercapto-ethyl)-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 8 295 0.1M imidazole pH 8.0, 0.2M Ca(OAC)2, 10% PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.45 49.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.21 α = 90 b = 93.289 β = 90 c = 100.329 γ = 90
Symmetry Space Group P 21 21 21
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 210 2004-06-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.98 ALS 5.0.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.2 20 18114
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 2.2 20 15750 877 71.77 0.231 0.22889 0.2223 0.26859 0.2588 RANDOM 34.255
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] -3.48 0.47 3.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.689 r_dihedral_angle_4_deg 14.859 r_dihedral_angle_3_deg 13.418 r_dihedral_angle_1_deg 4.801 r_mcangle_it 1.75 r_scangle_it 1.312 r_mcbond_it 1.029 r_angle_refined_deg 0.873 r_scbond_it 0.815 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.689 r_dihedral_angle_4_deg 14.859 r_dihedral_angle_3_deg 13.418 r_dihedral_angle_1_deg 4.801 r_mcangle_it 1.75 r_scangle_it 1.312 r_mcbond_it 1.029 r_angle_refined_deg 0.873 r_scbond_it 0.815 r_nbtor_refined 0.301 r_nbd_refined 0.15 r_symmetry_hbond_refined 0.13 r_symmetry_vdw_refined 0.102 r_xyhbond_nbd_refined 0.081 r_chiral_restr 0.056 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 2903 Nucleic Acid Atoms Solvent Atoms 169 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection d*TREK data reduction d*TREK data scaling AMoRE phasing