6JSZ

BACE2 xaperone complex with N-{3-[(5R)-3-amino-5-methyl-9,9-dioxo-2,9lambda6-dithia-4-azaspiro[5.5]undec-3-en-5-yl]-4-fluorophenyl}-5-(fluoromethoxy)pyrazine-2-carboxamide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3ZKG 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8293.150.1M TRIS pH 8.0, 25% PEG 3350, pH 8.0
Crystal Properties
Matthews coefficientSolvent content
2.3146.76

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.542α = 90
b = 74.467β = 90
c = 109.135γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2016-06-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA1.0000SLSX06DA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Rrim I (All)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
11.5361.5199.50.0350.0419.094.178375
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Rrim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.531.7899.10.490.5634.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUT3ZKG1.5361.5174276409999.670.22580.22520.237RANDOM28.96
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]
-0.45-1.82.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.944
r_dihedral_angle_4_deg12.371
r_dihedral_angle_3_deg11.01
r_dihedral_angle_1_deg5.859
r_angle_refined_deg1.439
r_angle_other_deg1.187
r_chiral_restr0.079
r_bond_refined_d0.01
r_gen_planes_refined0.004
r_bond_other_d0.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.944
r_dihedral_angle_4_deg12.371
r_dihedral_angle_3_deg11.01
r_dihedral_angle_1_deg5.859
r_angle_refined_deg1.439
r_angle_other_deg1.187
r_chiral_restr0.079
r_bond_refined_d0.01
r_gen_planes_refined0.004
r_bond_other_d0.003
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3560
Nucleic Acid Atoms
Solvent Atoms299
Heterogen Atoms35

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing