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X-ray crystal structure of beta secretase complexed with compound 5
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 2.97 58.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.412 α = 90 b = 102.412 β = 90 c = 169.237 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 2002-10-24 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) 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 2.2 38.2 26905 24904
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 PDB entry 1W50 2.25 38.19 23631 1278 97.33 0.223 0.22 0.2256 0.28 0.2809 RANDOM 36.407
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] -0.37 -0.19 -0.37 0.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.126 r_dihedral_angle_3_deg 14.774 r_dihedral_angle_4_deg 12.739 r_dihedral_angle_1_deg 6.986 r_angle_refined_deg 1.407 r_angle_other_deg 0.89 r_symmetry_vdw_other 0.251 r_nbd_other 0.204 r_nbd_refined 0.193 r_symmetry_vdw_refined 0.188
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.126 r_dihedral_angle_3_deg 14.774 r_dihedral_angle_4_deg 12.739 r_dihedral_angle_1_deg 6.986 r_angle_refined_deg 1.407 r_angle_other_deg 0.89 r_symmetry_vdw_other 0.251 r_nbd_other 0.204 r_nbd_refined 0.193 r_symmetry_vdw_refined 0.188 r_nbtor_refined 0.185 r_xyhbond_nbd_refined 0.147 r_symmetry_hbond_refined 0.113 r_nbtor_other 0.089 r_scangle_it 0.089 r_chiral_restr 0.079 r_mcangle_it 0.076 r_scbond_it 0.073 r_mcbond_it 0.055 r_mcbond_other 0.021 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 179 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection MOSFLM data reduction CCP4 data scaling CSearch phasing