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Crystal structure of human beta-secretase in complex with NVP-ARV999
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DUY PDB entry 3DUY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 1.0M Ammonium sulfate in water, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K. Protein stock was BACE 7.3 mg/mL in 10mM Tris-HCl pH 7.4, 25mM NaCl. Crystals were grown in 96-well Corning Microtiter plates. Cryo-protectant was 80% well solution, 20% 1,2-Propanediol
Crystal Properties Matthews coefficient Solvent content 3.05 59.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.027 α = 90 b = 102.945 β = 103.66 c = 99.916 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 95 CCD MAR CCD 165 mm 2003-03-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.95371 SLS X06SA
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 2.1 100 100 0.056 12.1 4.3 93176 93176 30.8
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) 2.1 2.18 100 0.309 9252
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 FOURIER SYNTHESIS THROUGHOUT PDB entry 3DUY 2.1 55.52 93153 93153 9307 99.4 0.223 0.223 0.207 0.2074 0.241 0.2398 RANDOM 46.843
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] -2.89 1.51 4.37 -1.48
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 25 c_scangle_it 4.25 c_mcangle_it 3.26 c_scbond_it 3.05 c_mcbond_it 2.18 c_angle_deg 1.3 c_improper_angle_d 0.76 c_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8934 Nucleic Acid Atoms Solvent Atoms 525 Heterogen Atoms 93
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling CNS refinement PDB_EXTRACT data extraction MAR345 data collection CNX phasing CNX refinement