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X-ray crystal structure of beta secretase complexed with compound 6b
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 2.81 56.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.303 α = 90 b = 101.303 β = 90 c = 170.355 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 2004-02-23 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 2.45 50.65 95.8 0.118 18681 18681
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 2.45 50.65 18681 18681 947 94.89 0.185 0.185 0.182 0.1876 0.251 0.2522 RANDOM 24.868
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] -0.93 -0.46 -0.93 1.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.052 r_dihedral_angle_4_deg 17.123 r_dihedral_angle_3_deg 16.474 r_dihedral_angle_1_deg 6.872 r_angle_refined_deg 1.478 r_angle_other_deg 0.988 r_symmetry_vdw_other 0.254 r_nbd_refined 0.208 r_nbd_other 0.205 r_symmetry_vdw_refined 0.197
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.052 r_dihedral_angle_4_deg 17.123 r_dihedral_angle_3_deg 16.474 r_dihedral_angle_1_deg 6.872 r_angle_refined_deg 1.478 r_angle_other_deg 0.988 r_symmetry_vdw_other 0.254 r_nbd_refined 0.208 r_nbd_other 0.205 r_symmetry_vdw_refined 0.197 r_nbtor_refined 0.191 r_xyhbond_nbd_refined 0.185 r_chiral_restr 0.154 r_scangle_it 0.127 r_symmetry_hbond_refined 0.118 r_scbond_it 0.1 r_mcangle_it 0.091 r_nbtor_other 0.089 r_mcbond_it 0.062 r_mcbond_other 0.022 r_bond_refined_d 0.013 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2948 Nucleic Acid Atoms Solvent Atoms 209 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction ProDC data collection MOSFLM data reduction CCP4 data scaling CSearch phasing