5I3W

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1W50 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION6.629820% polyethylene glycol 5000 MME, 200 mM ammonium iodide, 170 mM sodium citrate (pH 6.6), 3% DMSO
Crystal Properties
Matthews coefficientSolvent content
2.8156.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.66α = 90
b = 101.66β = 90
c = 172.357γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2011-11-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.21.0000ALS5.0.2

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
12.155099.90.13613.613.929496-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.152.2399.92.112.3

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 REPLACEMENTTHROUGHOUT1W502.155027785147099.60.18180.17990.2149RANDOM25.301
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]
-0.06-0.03-0.060.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.253
r_dihedral_angle_4_deg16.484
r_dihedral_angle_3_deg12.183
r_dihedral_angle_1_deg6.436
r_angle_refined_deg1.26
r_angle_other_deg0.816
r_chiral_restr0.069
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.253
r_dihedral_angle_4_deg16.484
r_dihedral_angle_3_deg12.183
r_dihedral_angle_1_deg6.436
r_angle_refined_deg1.26
r_angle_other_deg0.816
r_chiral_restr0.069
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 Atoms2968
Nucleic Acid Atoms
Solvent Atoms321
Heterogen Atoms49

Software

Software
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction