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Fragment Based Discovery and Optimisation of BACE-1 Inhibitors
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1W50 PDB ENTRY 1W50
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.6 273 20% PEG 5000MME 180mM Ammonium Iodide and 180mM Sodium Citrate pH6.6 , VAPOR DIFFUSION, HANGING DROP, temperature 273K
Crystal Properties Matthews coefficient Solvent content 2.76 55.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.19 α = 90 b = 100.19 β = 90 c = 172.84 γ = 120
Symmetry Space Group P 61 2 2
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 315r 2008-09-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.4 61.2 86.3 0.102 0.106 12.9 11.89 17067 2 40.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.46 89.5 0.287 0.131 4.3 11.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 PDB ENTRY 1W50 2.4 50.1 2 17938 17067 870 86.4 0.228 0.228 0.2237 0.235 0.2401 RANDOM 24.11
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] -0.72 -0.36 -0.72 1.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.79 r_dihedral_angle_4_deg 14.17 r_dihedral_angle_3_deg 13.727 r_dihedral_angle_1_deg 5.434 r_angle_refined_deg 1.036 r_mcangle_it 0.59 r_scangle_it 0.332 r_mcbond_it 0.328 r_scbond_it 0.184 r_chiral_restr 0.068
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.79 r_dihedral_angle_4_deg 14.17 r_dihedral_angle_3_deg 13.727 r_dihedral_angle_1_deg 5.434 r_angle_refined_deg 1.036 r_mcangle_it 0.59 r_scangle_it 0.332 r_mcbond_it 0.328 r_scbond_it 0.184 r_chiral_restr 0.068 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined 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 2965 Nucleic Acid Atoms Solvent Atoms 159 Heterogen Atoms 27
Software Software Software Name Purpose DNA data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling