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X-ray crystal structure of beta secretase complexed with 4-(4-fluorobenzyl)piperidine
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 2.87 57.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.388 α = 90 b = 102.388 β = 90 c = 170.232 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 2003-02-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-3 0.93300 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 2.15 47.79 99.6 0.085 29243 29243
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 2.15 47.79 29243 29243 1487 99.44 0.231 0.231 0.228 0.2364 0.285 0.2907 RANDOM 35.333
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] -0.65 -0.33 -0.65 0.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.702 r_dihedral_angle_3_deg 15.274 r_dihedral_angle_4_deg 12.848 r_dihedral_angle_1_deg 7.631 r_angle_refined_deg 1.388 r_angle_other_deg 0.882 r_symmetry_hbond_refined 0.297 r_symmetry_vdw_other 0.27 r_symmetry_vdw_refined 0.227 r_nbd_other 0.207
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.702 r_dihedral_angle_3_deg 15.274 r_dihedral_angle_4_deg 12.848 r_dihedral_angle_1_deg 7.631 r_angle_refined_deg 1.388 r_angle_other_deg 0.882 r_symmetry_hbond_refined 0.297 r_symmetry_vdw_other 0.27 r_symmetry_vdw_refined 0.227 r_nbd_other 0.207 r_nbd_refined 0.205 r_nbtor_refined 0.185 r_xyhbond_nbd_refined 0.179 r_scangle_it 0.088 r_nbtor_other 0.087 r_xyhbond_nbd_other 0.086 r_chiral_restr 0.079 r_mcangle_it 0.076 r_scbond_it 0.071 r_mcbond_it 0.055 r_mcbond_other 0.022 r_bond_refined_d 0.012 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 236 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction ADSC data collection MOSFLM data reduction CCP4 data scaling CSearch phasing