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BACE (Beta Secretase) in complex with a nanomolar non-peptidic inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1W50 PDB ENTRY 1W50
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.6 pH 6.60
Crystal Properties Matthews coefficient Solvent content 2.77 55.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.351 α = 90 b = 102.351 β = 90 c = 168 γ = 120
Symmetry Space Group P 61 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS 4 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300
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 2.55 39 99.6 0.11 4.5 3.2 16609
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 2.55 2.69 99 0.46 1.6
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 1W50 2.55 39.2 16609 890 99.4 0.219 0.216 0.2206 0.288 0.2847 RANDOM 46.79
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] -0.94 -0.47 -0.94 1.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 8.274 r_scangle_it 5.464 r_mcangle_it 4.666 r_scbond_it 3.762 r_mcbond_it 3.131 r_angle_refined_deg 1.681 r_angle_other_deg 0.906 r_symmetry_hbond_refined 0.366 r_symmetry_vdw_refined 0.302 r_symmetry_vdw_other 0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 8.274 r_scangle_it 5.464 r_mcangle_it 4.666 r_scbond_it 3.762 r_mcbond_it 3.131 r_angle_refined_deg 1.681 r_angle_other_deg 0.906 r_symmetry_hbond_refined 0.366 r_symmetry_vdw_refined 0.302 r_symmetry_vdw_other 0.25 r_nbd_other 0.241 r_nbd_refined 0.219 r_xyhbond_nbd_refined 0.217 r_chiral_restr 0.089 r_nbtor_other 0.087 r_bond_refined_d 0.017 r_gen_planes_refined 0.006 r_gen_planes_other 0.003 r_bond_other_d 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2946 Nucleic Acid Atoms Solvent Atoms 140 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling AMoRE phasing