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Crystal structure of human beta-secretase in complex with NVP-AFJ144
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FKN PDB entry 1FKN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 1.0M Ammonium sulfate in water, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K. Protein stock was BACE MUT46B batch XII 8.5 mg/mL in 10mM Tris-HCl pH 7.4, 25mM NaCl, with a 5-fold excess of NVP-AFJ144-NX-2 added from a 50mM stock solution in 90% DMSO-D6 (1.8% DMSO in drop). A solution containing 1.2M Ammonium sulfate, 25% Glycerol, 1mM NVP-AFJ144-NX-2 and 1.8% DMSO was used as cryo-protectant
Crystal Properties Matthews coefficient Solvent content 3.1 60.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.537 α = 90 b = 103.062 β = 103.64 c = 100.602 γ = 90
Symmetry Space Group P 1 21 1
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 RIGAKU SATURN 92 Mirrors 2005-11-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.54178
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 1.97 70.93 93.5 0.068 22.55 10.2 107931 107931 -3 33.092
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) 1.97 2.03 61.7 0.395 3.8 4.7 6065
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 1FKN 1.97 70.93 107931 107931 10413 93.4 0.204 0.204 0.202 0.2023 0.223 0.2233 RANDOM 35.063
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] -1.27 -0.09 2.16 -0.89
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.5 c_scangle_it 3.02 c_mcangle_it 2.34 c_scbond_it 2 c_mcbond_it 1.47 c_angle_deg 0.8 c_improper_angle_d 0.62 c_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8777 Nucleic Acid Atoms Solvent Atoms 750 Heterogen Atoms 99
Software Software Software Name Purpose XSCALE data scaling CNS refinement PDB_EXTRACT data extraction XDS data reduction CNX phasing CNX refinement