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Structure of Bace (beta secretase) in complex with ligand EV2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2B8L PDB ENTRY 2B8L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6 295 10% PEG 4000, 100mM MES pH 6.0, VAPOR DIFFUSION, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.57 52.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 230.625 α = 90 b = 99.88 β = 103.12 c = 62.9 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 100 CCD MARMOSAIC 225 mm CCD 2008-01-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 0.9999 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.48 48.8 98.3 0.047 0.047 14.82 3.3 47564 48552 2 2 20.736
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.48 2.57 96.2 0.657 0.657 3.01 3.2 4849
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2B8L 2.48 48.8 2 2 48570 47564 986 100 0.22703 0.226 0.22585 0.2264 0.28115 0.2789 RANDOM 20.736
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] -7.7 -0.13 -5.13 12.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.663 r_dihedral_angle_4_deg 20.226 r_dihedral_angle_3_deg 15.73 r_dihedral_angle_1_deg 6.727 r_scangle_it 2.145 r_scbond_it 1.45 r_angle_refined_deg 1.21 r_angle_other_deg 1.17 r_mcangle_it 1.075 r_mcbond_it 0.869
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.663 r_dihedral_angle_4_deg 20.226 r_dihedral_angle_3_deg 15.73 r_dihedral_angle_1_deg 6.727 r_scangle_it 2.145 r_scbond_it 1.45 r_angle_refined_deg 1.21 r_angle_other_deg 1.17 r_mcangle_it 1.075 r_mcbond_it 0.869 r_symmetry_vdw_other 0.281 r_nbd_other 0.192 r_symmetry_vdw_refined 0.191 r_nbd_refined 0.189 r_nbtor_refined 0.183 r_xyhbond_nbd_refined 0.156 r_symmetry_hbond_refined 0.104 r_mcbond_other 0.093 r_nbtor_other 0.083 r_chiral_restr 0.071 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_xyhbond_nbd_other 0.004 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8784 Nucleic Acid Atoms Solvent Atoms 117 Heterogen Atoms 54
Software Software Software Name Purpose SLSPX data collection REFMAC refinement XDS data reduction XSCALE data scaling