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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 7.5 298 1.5M LITHIUM SULFATE, 0.1M HEPES BUFFER, Crystals were grown with L124671 and L304507 was back soak, pH 7.50, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.83 56.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.795 α = 90 b = 127.13 β = 90 c = 76.205 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++ 2003-12-15 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 1.6 50 87.5 0.083 17.9 3.2 32116
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.6 1.66 35 0.5 1.5
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 2 50 32116 1763 98.5 0.19524 0.19402 0.21795 RANDOM 31.045
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] -1.2 3.52 -2.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.622 r_dihedral_angle_4_deg 23.721 r_dihedral_angle_3_deg 13.572 r_dihedral_angle_1_deg 6.12 r_scangle_it 2.557 r_scbond_it 1.566 r_angle_refined_deg 1.228 r_mcangle_it 1.205 r_mcbond_it 0.719 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.622 r_dihedral_angle_4_deg 23.721 r_dihedral_angle_3_deg 13.572 r_dihedral_angle_1_deg 6.12 r_scangle_it 2.557 r_scbond_it 1.566 r_angle_refined_deg 1.228 r_mcangle_it 1.205 r_mcbond_it 0.719 r_nbtor_refined 0.309 r_symmetry_vdw_refined 0.2 r_nbd_refined 0.193 r_symmetry_hbond_refined 0.147 r_xyhbond_nbd_refined 0.118 r_chiral_restr 0.084 r_bond_refined_d 0.01 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 2922 Nucleic Acid Atoms Solvent Atoms 211 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing