☰ Navigation Tabs
X-ray crystal structure of beta secretase complexed with compound 3
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 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, pH 6.60
Crystal Properties Matthews coefficient Solvent content 2.86 56.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.541 α = 90 b = 102.541 β = 90 c = 169.062 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 2003-04-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
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 47.58 0.091 25567
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 (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 47.58 25567 25567 1304 99.7 0.234 0.232 0.2379 0.281 0.2849 RANDOM 36.79
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] -0.21 -0.1 -0.21 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.623 r_dihedral_angle_4_deg 17.285 r_dihedral_angle_3_deg 16.014 r_dihedral_angle_1_deg 7.212 r_angle_refined_deg 1.421 r_angle_other_deg 0.901 r_symmetry_vdw_other 0.24 r_symmetry_vdw_refined 0.237 r_nbd_other 0.207 r_nbd_refined 0.198
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.623 r_dihedral_angle_4_deg 17.285 r_dihedral_angle_3_deg 16.014 r_dihedral_angle_1_deg 7.212 r_angle_refined_deg 1.421 r_angle_other_deg 0.901 r_symmetry_vdw_other 0.24 r_symmetry_vdw_refined 0.237 r_nbd_other 0.207 r_nbd_refined 0.198 r_nbtor_refined 0.187 r_xyhbond_nbd_refined 0.139 r_symmetry_hbond_refined 0.134 r_scangle_it 0.097 r_nbtor_other 0.089 r_mcangle_it 0.082 r_chiral_restr 0.08 r_scbond_it 0.078 r_mcbond_it 0.06 r_mcbond_other 0.024 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2966 Nucleic Acid Atoms Solvent Atoms 123 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction CCP4 data scaling CSearch phasing