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X-ray crystal structure of beta secretase complexed with compound 8b
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 VAPOR DIFFUSION, HANGING DROP 6.6 293 20-22.5% (w/v) PEG 5000 monomethylether (MME), 200 mM sodium citrate (pH 6.6), 200 mM ammonium iodide, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.83 56.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.162 α = 90 b = 102.162 β = 90 c = 168.385 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 IMAGE PLATE RIGAKU RAXIS IV 2004-01-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.54180
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 2.35 37.78 98.3 0.081 21939 21939
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2.35 37.78 21939 21939 1128 98.29 0.198 0.198 0.195 0.2018 0.248 0.2488 RANDOM 36.048
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] -0.74 -0.37 -0.74 1.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.628 r_dihedral_angle_4_deg 17.914 r_dihedral_angle_3_deg 15.831 r_dihedral_angle_1_deg 6.82 r_angle_refined_deg 1.409 r_angle_other_deg 0.893 r_nbd_other 0.206 r_symmetry_vdw_refined 0.205 r_symmetry_vdw_other 0.201 r_nbd_refined 0.193
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.628 r_dihedral_angle_4_deg 17.914 r_dihedral_angle_3_deg 15.831 r_dihedral_angle_1_deg 6.82 r_angle_refined_deg 1.409 r_angle_other_deg 0.893 r_nbd_other 0.206 r_symmetry_vdw_refined 0.205 r_symmetry_vdw_other 0.201 r_nbd_refined 0.193 r_symmetry_hbond_refined 0.193 r_nbtor_refined 0.186 r_xyhbond_nbd_refined 0.156 r_nbtor_other 0.088 r_scangle_it 0.084 r_chiral_restr 0.082 r_scbond_it 0.069 r_mcangle_it 0.068 r_mcbond_it 0.047 r_mcbond_other 0.018 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2966 Nucleic Acid Atoms Solvent Atoms 161 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection MOSFLM data reduction CCP4 data scaling CSearch phasing