4FRI

Crystal structure of BACE1 in complex with biarylspiro aminooxazoline 6


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.629320% PEG 5000 monomethyl ether, 200 mM ammonium iodide, 180 mM sodium citrate (pH 6.6), VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.7655.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.461α = 90
b = 101.461β = 90
c = 170.689γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++Varimax HR2008-02-22MSINGLE 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
12.33096.70.1437.610.22383423047-348.1
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)
12.32.3894.30.9168.82183

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1W502.3302378723045167696.880.20090.19740.2459RANDOM38.7276
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]
0.090.050.09-0.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.725
r_dihedral_angle_4_deg17.018
r_dihedral_angle_3_deg13.772
r_dihedral_angle_1_deg6.628
r_angle_refined_deg1.233
r_angle_other_deg0.821
r_chiral_restr0.069
r_bond_refined_d0.008
r_gen_planes_refined0.004
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.725
r_dihedral_angle_4_deg17.018
r_dihedral_angle_3_deg13.772
r_dihedral_angle_1_deg6.628
r_angle_refined_deg1.233
r_angle_other_deg0.821
r_chiral_restr0.069
r_bond_refined_d0.008
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2931
Nucleic Acid Atoms
Solvent Atoms213
Heterogen Atoms34

Software

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