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Crystal Structure of Human BACE-1 in Complex with Compound 38a (NB-854)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4D88
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 292 15% PEG 1,500 in water
Crystal Properties Matthews coefficient Solvent content 2.13 42.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.576 α = 90 b = 74.805 β = 90 c = 104.974 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 100 CCD RIGAKU SATURN 92 mirrors 2010-01-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.54178
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.77 60.92 90.8 0.051 0.056 24.66 5.998 34586 -3 11
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.77 1.83 52.1 0.166 0.209 5.89 2.431
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 4D88 1.77 60.92 34586 1730 90.7 0.186 0.1785 0.211 0.2042 RANDOM 16.1
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] 0.46 0.75 -1.21
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.1 c_scangle_it 3.11 c_mcangle_it 2.14 c_scbond_it 2.08 c_mcbond_it 1.36 c_angle_deg 0.9 c_improper_angle_d 0.62 c_bond_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2969 Nucleic Acid Atoms Solvent Atoms 336 Heterogen Atoms 29
Software Software Software Name Purpose XDS data reduction XSCALE data scaling CNS refinement PDB_EXTRACT data extraction CNS phasing