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Crystal structure of human beta-secretase in complex with NVP-BAV544
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DV1 PDB entry 3DV1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 1.0M Ammonium phosphate, 0.1M Sodium citrate, VAPOR DIFFUSION, HANGING DROP, pH 5.1, temperature 292K. Protein stock was BACE 8.45 mg/mL in 10mM Tris-HCl pH 7.4, 25mM NaCl, with a 3.8-fold excess of NVP-BAV544-AA-1 added from a 50mM stock solution in DMSO (1.4% DMSO in drop). Cryo-protectant was 20% v/v 1,2-Propanediol, 80% Reservoir solution
Crystal Properties Matthews coefficient Solvent content 3.04 59.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.661 α = 90 b = 103.353 β = 103.72 c = 99.474 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 96 CCD MAR CCD 165 mm 2004-04-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.97933 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 99.5 0.068 8.5 6.3 94339 94339 33
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 95.7 0.402 9020
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 3DV1 2.1 55.23 93604 93604 9360 99.9 0.211 0.211 0.192 0.1922 0.221 0.221 RANDOM 50.342
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] -0.14 1.75 7.01 -6.87
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 25.2 c_scangle_it 4.22 c_mcangle_it 3.03 c_scbond_it 2.99 c_mcbond_it 2.02 c_angle_deg 1.4 c_improper_angle_d 0.79 c_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8925 Nucleic Acid Atoms Solvent Atoms 453 Heterogen Atoms 105
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling CNS refinement PDB_EXTRACT data extraction MAR345 data collection CNX phasing CNX refinement