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Crystal Structure of Human Beta Secretase Complexed with inhibitor
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 Crystals were grown with L124671 and inhibitor was back soaked in the crystal at pH 5.0. 1.5M LITHIUM SULFATE, 0.1M HEPES BUFFER, pH 7.50, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.82 56.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.811 α = 90 b = 128.523 β = 90 c = 76.276 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++ 2007-03-15 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 1.7 30 100 0.046 36.3 6.2 56340
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) 1.7 1.76 100 0.49 3.4 5.9
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 1.7 30 53441 2857 99.92 0.18596 0.18501 0.20387 RANDOM 27.379
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] -1.11 2.27 -1.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.11 r_dihedral_angle_4_deg 21.277 r_dihedral_angle_3_deg 12.232 r_dihedral_angle_1_deg 5.962 r_scangle_it 3.111 r_scbond_it 1.939 r_mcangle_it 1.352 r_angle_refined_deg 1.215 r_mcbond_it 0.851 r_nbtor_refined 0.313
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.11 r_dihedral_angle_4_deg 21.277 r_dihedral_angle_3_deg 12.232 r_dihedral_angle_1_deg 5.962 r_scangle_it 3.111 r_scbond_it 1.939 r_mcangle_it 1.352 r_angle_refined_deg 1.215 r_mcbond_it 0.851 r_nbtor_refined 0.313 r_nbd_refined 0.191 r_symmetry_vdw_refined 0.19 r_symmetry_hbond_refined 0.137 r_xyhbond_nbd_refined 0.12 r_chiral_restr 0.084 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 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 2871 Nucleic Acid Atoms Solvent Atoms 293 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing