6JSN

Crystal Structure of BACE1 in 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 1W50 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5293.150.2 M sodium citrate, 0.2 M ammonium iodide, 19%(w/v) polyethylene glycol 5000 monomethyl ether, pH 6.5
Crystal Properties
Matthews coefficientSolvent content
359.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.705α = 90
b = 101.705β = 90
c = 170.422γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2016-07-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.54178

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
12.65099.70.1822.37.316705
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)
12.62.640.553

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 REPLACEMENTTHROUGHOUT1W502.62014939168099.510.20630.20060.2585RANDOM44.745
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]
-0.15-0.08-0.150.49
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.263
r_dihedral_angle_3_deg16.688
r_dihedral_angle_4_deg12.54
r_dihedral_angle_1_deg6.819
r_angle_other_deg2.124
r_angle_refined_deg1.544
r_chiral_restr0.091
r_bond_refined_d0.01
r_bond_other_d0.005
r_gen_planes_refined0.005
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.263
r_dihedral_angle_3_deg16.688
r_dihedral_angle_4_deg12.54
r_dihedral_angle_1_deg6.819
r_angle_other_deg2.124
r_angle_refined_deg1.544
r_chiral_restr0.091
r_bond_refined_d0.01
r_bond_other_d0.005
r_gen_planes_refined0.005
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2920
Nucleic Acid Atoms
Solvent Atoms77
Heterogen Atoms46

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing