3R2F

Crystal structure of beta-site app-cleaving enzyme 1 (BACE-WT) complex with BMS-693391 AKA (2S)-2-((3R)-3-acetamido-3-isobutyl-2-oxo-1-pyrrolidinyl)-N-((1S,2R)-1-(3,5-difluorobenzyl)-2-hydroxy-2-((2R,4R)-4-propoxy-2-pyrrolidinyl)ethyl)-4-phenylbutanamide


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.229814% PEG8000, 0.2 M ammonium sulfate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.4249.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 86.306α = 90
b = 130.255β = 96.53
c = 86.927γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 922004-01-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E SUPERBRIGHT

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.52986.38799.60.110.1112.43.5629283.1
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.552.6499.60.3153.13.2

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 REPLACEMENTTHROUGHOUT2.5359696319498.640.282660.280110.33002RANDOM22.761
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]
-2.1-0.25-2.544.59
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.547
r_dihedral_angle_3_deg16.853
r_dihedral_angle_4_deg16.157
r_dihedral_angle_1_deg6.736
r_scangle_it1.762
r_angle_refined_deg1.426
r_scbond_it1.103
r_mcangle_it0.992
r_mcbond_it0.577
r_symmetry_vdw_refined0.51
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.547
r_dihedral_angle_3_deg16.853
r_dihedral_angle_4_deg16.157
r_dihedral_angle_1_deg6.736
r_scangle_it1.762
r_angle_refined_deg1.426
r_scbond_it1.103
r_mcangle_it0.992
r_mcbond_it0.577
r_symmetry_vdw_refined0.51
r_symmetry_hbond_refined0.43
r_nbtor_refined0.314
r_nbd_refined0.217
r_xyhbond_nbd_refined0.167
r_chiral_restr0.106
r_bond_refined_d0.009
r_gen_planes_refined0.004
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 Atoms122
Heterogen Atoms188

Software

Software
Software NamePurpose
REFMACrefinement
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing