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Crystal Structure of Human Beta Secretase Complexed with Spiropiperdine Iminohydantoin Inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TQF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5 293 1.5M LITHIUM SULFATE, 0.1M HEPES BUFFER, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K, PH 7.50. Crystals were grown with L124671 and spiropiperdine iminoh was back soaked in the crystal at pH 5.0, pH 5.00
Crystal Properties Matthews coefficient Solvent content 2.83 56.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.743 α = 90 b = 128.042 β = 90 c = 76.768 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 1.9 50 99.9 0.067 6.8 40623
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) 1.9 1.97 99.8 0.568 2.4 6.3
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 1TQF 1.9 42.99 38567 2034 99.84 0.18332 0.1816 0.178 0.21663 0.2101 RANDOM 32.33
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] 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.768 r_dihedral_angle_4_deg 16.688 r_dihedral_angle_3_deg 14.381 r_dihedral_angle_1_deg 7.55 r_scangle_it 3.331 r_scbond_it 2.109 r_mcangle_it 1.516 r_angle_refined_deg 1.438 r_mcbond_it 0.917 r_symmetry_hbond_refined 0.366
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.768 r_dihedral_angle_4_deg 16.688 r_dihedral_angle_3_deg 14.381 r_dihedral_angle_1_deg 7.55 r_scangle_it 3.331 r_scbond_it 2.109 r_mcangle_it 1.516 r_angle_refined_deg 1.438 r_mcbond_it 0.917 r_symmetry_hbond_refined 0.366 r_nbtor_refined 0.31 r_nbd_refined 0.203 r_symmetry_vdw_refined 0.202 r_xyhbond_nbd_refined 0.163 r_chiral_restr 0.096 r_bond_refined_d 0.013 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2895 Nucleic Acid Atoms Solvent Atoms 342 Heterogen Atoms 36
Software Software Software Name Purpose CCP4 model building REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling CCP4 phasing