4XKX

Crystal structure of BACE1 in complex with 2-aminooxazoline 3-azaxanthene inhibitor 28


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4FRKPDB entry 4FRK

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.629820% polyethylene glycol 5000 MME, 200 mM ammonium iodide, 170 mM sodium citrate, pH 6.6, 3% dimethylsulfoxide, apo crystals soaked with 1 mM inhibitor for 4 h
Crystal Properties
Matthews coefficientSolvent content
2.8156.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102.148α = 90
b = 102.148β = 90
c = 170.894γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2010-03-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E SUPERBRIGHT1.5418

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
11.85085.90.058207.44951242531-328.01
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)
11.81.8643.50.5383.083.22098

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 DIFFRACTIONTHROUGHOUTPDB entry 4FRK1.85042507217585.980.19410.19230.2281RANDOM25.32
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]
0.020.010.02-0.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.848
r_dihedral_angle_4_deg16.017
r_dihedral_angle_3_deg12.113
r_dihedral_angle_1_deg6.416
r_angle_refined_deg1.234
r_angle_other_deg0.825
r_chiral_restr0.07
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.848
r_dihedral_angle_4_deg16.017
r_dihedral_angle_3_deg12.113
r_dihedral_angle_1_deg6.416
r_angle_refined_deg1.234
r_angle_other_deg0.825
r_chiral_restr0.07
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2869
Nucleic Acid Atoms
Solvent Atoms423
Heterogen Atoms49

Software

Software
Software NamePurpose
CrystalCleardata collection
REFMACrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling