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Potent beta-secretase 1 inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DM6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 299 16% PEG8000, 0.1M citrate, 0.3M lithium sulphate, 0.1M sodium chloride, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 299K
Crystal Properties Matthews coefficient Solvent content 3.04 59.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.838 α = 90 b = 103.075 β = 103.32 c = 100.499 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray IMAGE PLATE RIGAKU RAXIS IV 2006-09-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.5 97.59 99.7 53317 38.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.5 2.56 100
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 3DM6 2.5 40.26 53317 2849 99.7 0.232 0.229 0.2242 0.282 0.2746 RANDOM 38.2
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] -0.13 -0.17 0.37 -0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.703 r_dihedral_angle_4_deg 18.528 r_dihedral_angle_3_deg 16.896 r_dihedral_angle_1_deg 8.076 r_scangle_it 5.697 r_scbond_it 4.002 r_mcangle_it 2.709 r_angle_refined_deg 1.992 r_mcbond_it 1.672 r_nbtor_refined 0.335
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.703 r_dihedral_angle_4_deg 18.528 r_dihedral_angle_3_deg 16.896 r_dihedral_angle_1_deg 8.076 r_scangle_it 5.697 r_scbond_it 4.002 r_mcangle_it 2.709 r_angle_refined_deg 1.992 r_mcbond_it 1.672 r_nbtor_refined 0.335 r_symmetry_vdw_refined 0.281 r_nbd_refined 0.233 r_chiral_restr 0.146 r_xyhbond_nbd_refined 0.141 r_symmetry_hbond_refined 0.04 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 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 8805 Nucleic Acid Atoms Solvent Atoms 71 Heterogen Atoms 180
Software Software Software Name Purpose AMoRE phasing REFMAC refinement MOSFLM data reduction SCALA data scaling