☰ Navigation Tabs
X-ray crystal structure of beta secretase complexed with compound 24
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 20-22.5% (W/V) PEG 5000 MONOMETHYLETHYL (MME), 200 MM SODIUM CITRATE (PH 6.6) AND 200 MM AMMONIUM IODIDE
Crystal Properties Matthews coefficient Solvent content 3.06 59.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.971 α = 90 b = 102.971 β = 90 c = 167.28 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 CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
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 2.5 47 99.9 0.07 2.5 17850
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.56 100 0.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 2.5 47.28 17805 964 99.8 0.228 0.224 0.2289 0.289 0.2876 RANDOM 39.45
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.808 r_dihedral_angle_4_deg 16.734 r_dihedral_angle_3_deg 16.191 r_dihedral_angle_1_deg 8.205 r_angle_refined_deg 1.48 r_angle_other_deg 0.903 r_symmetry_vdw_other 0.222 r_nbd_refined 0.217 r_nbd_other 0.21 r_nbtor_refined 0.191
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.808 r_dihedral_angle_4_deg 16.734 r_dihedral_angle_3_deg 16.191 r_dihedral_angle_1_deg 8.205 r_angle_refined_deg 1.48 r_angle_other_deg 0.903 r_symmetry_vdw_other 0.222 r_nbd_refined 0.217 r_nbd_other 0.21 r_nbtor_refined 0.191 r_symmetry_vdw_refined 0.178 r_xyhbond_nbd_refined 0.144 r_scangle_it 0.095 r_nbtor_other 0.09 r_chiral_restr 0.088 r_mcangle_it 0.076 r_scbond_it 0.072 r_symmetry_hbond_refined 0.067 r_mcbond_it 0.051 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d 0.001 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2961 Nucleic Acid Atoms Solvent Atoms 88 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling CSearch phasing