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Crystal Structure of human Beta Secretase complexed with IXS
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TQF PDB entry 1TQF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 1.5M LITHIUM SULFATE, 0.1M HEPES BUFFER,
Crystals were grown with inhibitors were back soaked, pH 7.50, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.8 56.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.931 α = 90 b = 128.152 β = 90 c = 76.307 γ = 90
Symmetry Space Group C 2 2 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 IMAGE PLATE RIGAKU RAXIS IV++ M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.8 50 99.3 0.053 28.5 4.5 47976
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.8 1.86 99 0.52 5.3 4
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1TQF 1.8 20 40677 2169 89.33 0.21746 0.21621 0.24107 RANDOM 19.496
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] -0.75 2.06 -1.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.794 r_dihedral_angle_4_deg 22.947 r_dihedral_angle_3_deg 14.412 r_dihedral_angle_1_deg 5.984 r_scangle_it 2.2 r_scbond_it 1.374 r_angle_refined_deg 1.176 r_mcangle_it 0.961 r_mcbond_it 0.581 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.794 r_dihedral_angle_4_deg 22.947 r_dihedral_angle_3_deg 14.412 r_dihedral_angle_1_deg 5.984 r_scangle_it 2.2 r_scbond_it 1.374 r_angle_refined_deg 1.176 r_mcangle_it 0.961 r_mcbond_it 0.581 r_nbtor_refined 0.31 r_nbd_refined 0.193 r_symmetry_hbond_refined 0.193 r_symmetry_vdw_refined 0.17 r_xyhbond_nbd_refined 0.119 r_chiral_restr 0.08 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 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 2961 Nucleic Acid Atoms Solvent Atoms 411 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement d*TREK data reduction d*TREK data scaling REFMAC phasing