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X-ray crystal structure of beta secretase complexed with N~3~-benzylpyridine-2,3-diamine
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 56.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.172 α = 90 b = 101.172 β = 90 c = 170.924 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 4 2002-12-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX14.2 0.97800 SRS PX14.2
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 2.7 42.44 96.6 0.139 14335 14335
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 2.7 42.44 14335 14335 729 96.59 0.214 0.214 0.211 0.2154 0.279 0.2786 RANDOM 37.579
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] -0.98 -0.49 -0.98 1.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.681 r_dihedral_angle_3_deg 17.715 r_dihedral_angle_4_deg 15.095 r_dihedral_angle_1_deg 7.224 r_angle_refined_deg 1.43 r_angle_other_deg 0.868 r_nbd_refined 0.213 r_symmetry_vdw_other 0.211 r_nbd_other 0.204 r_nbtor_refined 0.193
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.681 r_dihedral_angle_3_deg 17.715 r_dihedral_angle_4_deg 15.095 r_dihedral_angle_1_deg 7.224 r_angle_refined_deg 1.43 r_angle_other_deg 0.868 r_nbd_refined 0.213 r_symmetry_vdw_other 0.211 r_nbd_other 0.204 r_nbtor_refined 0.193 r_symmetry_vdw_refined 0.188 r_symmetry_hbond_refined 0.161 r_xyhbond_nbd_refined 0.126 r_nbtor_other 0.09 r_scangle_it 0.09 r_chiral_restr 0.076 r_mcangle_it 0.074 r_scbond_it 0.069 r_mcbond_it 0.047 r_mcbond_other 0.014 r_bond_refined_d 0.012 r_xyhbond_nbd_other 0.012 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 2966 Nucleic Acid Atoms Solvent Atoms 75 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction ADSC data collection MOSFLM data reduction CCP4 data scaling CSearch phasing