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X-ray crystal structure of beta secretase complexed with compound 6a
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 56.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.03 α = 90 b = 101.03 β = 90 c = 172.33 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 MAR CCD 165 mm 2003-09-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-3 0.93100 ESRF ID14-3
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 2.25 50.52 98.7 0.105 24903 24903
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) 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 2.25 50.52 0.173 24903 24903 1271 98.11 0.173 0.17 0.1797 0.214 0.2171 RANDOM 25.206
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] -1.32 -0.66 -1.32 1.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.715 r_dihedral_angle_4_deg 16.602 r_dihedral_angle_3_deg 14.924 r_dihedral_angle_1_deg 7.085 r_angle_refined_deg 1.424 r_angle_other_deg 0.876 r_symmetry_vdw_other 0.238 r_xyhbond_nbd_refined 0.229 r_symmetry_hbond_refined 0.229 r_nbd_other 0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.715 r_dihedral_angle_4_deg 16.602 r_dihedral_angle_3_deg 14.924 r_dihedral_angle_1_deg 7.085 r_angle_refined_deg 1.424 r_angle_other_deg 0.876 r_symmetry_vdw_other 0.238 r_xyhbond_nbd_refined 0.229 r_symmetry_hbond_refined 0.229 r_nbd_other 0.21 r_nbd_refined 0.201 r_nbtor_refined 0.186 r_symmetry_vdw_refined 0.172 r_scangle_it 0.11 r_mcangle_it 0.093 r_scbond_it 0.091 r_nbtor_other 0.09 r_chiral_restr 0.085 r_mcbond_it 0.07 r_mcbond_other 0.031 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 279 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction ProDC data collection MOSFLM data reduction CCP4 data scaling CSearch phasing