3SKG

Crystal structure of beta-site app-cleaving enzyme 1 (BACE-WT) complex with (2S)-2-((3R)-3-acetamido-3-isobutyl-2-oxo-1-pyrrolidinyl)-N-((1S,2R)-1-(3,5-difluorobenzyl)-2-hydroxy-2-(1,2,3,4-tetrahydro-3-isoquinolinyl)ethyl)-4-phenylbutanamide


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.2298pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.4249.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 86.24α = 90
b = 130.451β = 96.65
c = 86.872γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 92MICROMAX CONFOCAL2009-06-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E+ DW

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.87830.62899.90.1724.65.942876
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.931000.5325.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.8830.62840650215998.770.259430.254670.34813RANDOM21.53
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]
-2.420.24-3.15.57
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.118
r_dihedral_angle_3_deg21.663
r_dihedral_angle_4_deg19.529
r_dihedral_angle_1_deg8.835
r_scangle_it3.641
r_angle_refined_deg2.504
r_scbond_it2.484
r_mcangle_it2.269
r_mcbond_it1.454
r_nbtor_refined0.333
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.118
r_dihedral_angle_3_deg21.663
r_dihedral_angle_4_deg19.529
r_dihedral_angle_1_deg8.835
r_scangle_it3.641
r_angle_refined_deg2.504
r_scbond_it2.484
r_mcangle_it2.269
r_mcbond_it1.454
r_nbtor_refined0.333
r_symmetry_vdw_refined0.304
r_nbd_refined0.274
r_xyhbond_nbd_refined0.226
r_symmetry_hbond_refined0.182
r_chiral_restr0.151
r_bond_refined_d0.029
r_gen_planes_refined0.009
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms12136
Nucleic Acid Atoms
Solvent Atoms106
Heterogen Atoms192

Software

Software
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing