☰ Navigation Tabs
X-ray crystal structure of beta secretase complexed with 2-aminoquinoline
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 57.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.833 α = 90 b = 102.833 β = 90 c = 168.85 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 2002-10-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX14.2 0.97000 SRS PX14.2
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 2.65 49.19 99.97 15979 15979
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 2.65 49.19 15979 15979 797 99.97 0.206 0.206 0.202 0.2054 0.282 0.2777 RANDOM 30.976
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] 0.29 0.14 0.29 -0.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.405 r_dihedral_angle_3_deg 15.588 r_dihedral_angle_4_deg 15.459 r_dihedral_angle_1_deg 6.795 r_angle_refined_deg 1.462 r_angle_other_deg 0.903 r_symmetry_hbond_refined 0.311 r_symmetry_vdw_other 0.252 r_nbd_refined 0.208 r_nbd_other 0.205
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.405 r_dihedral_angle_3_deg 15.588 r_dihedral_angle_4_deg 15.459 r_dihedral_angle_1_deg 6.795 r_angle_refined_deg 1.462 r_angle_other_deg 0.903 r_symmetry_hbond_refined 0.311 r_symmetry_vdw_other 0.252 r_nbd_refined 0.208 r_nbd_other 0.205 r_symmetry_vdw_refined 0.195 r_nbtor_refined 0.188 r_xyhbond_nbd_refined 0.157 r_scangle_it 0.128 r_scbond_it 0.109 r_mcangle_it 0.105 r_nbtor_other 0.089 r_chiral_restr 0.081 r_mcbond_it 0.069 r_xyhbond_nbd_other 0.05 r_mcbond_other 0.025 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 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 108 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction ADSC data collection MOSFLM data reduction CCP4 data scaling CSearch phasing