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Potent Beta-Secretase 1 hydroxyethylene Inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DM6 PDB ENTRY 3DM6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5 299 16% PEG8000, 0.1M Citrate, 0.3M Lithium sulphate, 0.1M Sodium Chloride, pH 5.0, VAPOR DIFFUSION, temperature 299K
Crystal Properties Matthews coefficient Solvent content 2.98 58.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.417 α = 90 b = 102.483 β = 103.53 c = 100.186 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 100 CCD ADSC QUANTUM 1 2007-10-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.98 ESRF ID14-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.1 102.6 95.8 0.055 15.1 3 89314 2 2 38
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.1 2.21 79.3 0.271 4.2 2.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3DM6 2.1 79.16 2 84864 4449 95.74 0.212 0.202 0.2 0.238 0.2573 RANDOM 37.954
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] 0.1 0.19 0.19 -0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.858 r_dihedral_angle_4_deg 18.883 r_dihedral_angle_3_deg 16.863 r_dihedral_angle_1_deg 7.934 r_scangle_it 4.24 r_scbond_it 2.81 r_mcangle_it 2.043 r_angle_refined_deg 1.886 r_mcbond_it 1.278 r_nbtor_refined 0.317
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.858 r_dihedral_angle_4_deg 18.883 r_dihedral_angle_3_deg 16.863 r_dihedral_angle_1_deg 7.934 r_scangle_it 4.24 r_scbond_it 2.81 r_mcangle_it 2.043 r_angle_refined_deg 1.886 r_mcbond_it 1.278 r_nbtor_refined 0.317 r_symmetry_vdw_refined 0.263 r_symmetry_hbond_refined 0.257 r_nbd_refined 0.22 r_xyhbond_nbd_refined 0.164 r_chiral_restr 0.145 r_bond_refined_d 0.019 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8820 Nucleic Acid Atoms Solvent Atoms 194 Heterogen Atoms 189
Software Software Software Name Purpose DNA data collection AMoRE phasing REFMAC refinement MOSFLM data reduction SCALA data scaling