5I3V

Crystal structure of BACE1 in complex with aminoquinoline compound 1


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, 0.2 M ammonium iodide, 0.17 M sodium citrate (pH 6.6), 3% DMSO
Crystal Properties
Matthews coefficientSolvent content
2.8456.76

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102.953α = 90
b = 102.953β = 90
c = 170.381γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2012-05-18MSINGLE 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
11.62501000.06721.816.168266-314.3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.621.681002.2613

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 REPLACEMENTTHROUGHOUT1W501.625064552342499.660.21020.20910.2312RANDOM16.294
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]
-0.04-0.02-0.040.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.486
r_dihedral_angle_4_deg14.103
r_dihedral_angle_3_deg10.915
r_dihedral_angle_1_deg6.431
r_angle_refined_deg1.273
r_angle_other_deg0.831
r_chiral_restr0.07
r_bond_refined_d0.008
r_gen_planes_refined0.006
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.486
r_dihedral_angle_4_deg14.103
r_dihedral_angle_3_deg10.915
r_dihedral_angle_1_deg6.431
r_angle_refined_deg1.273
r_angle_other_deg0.831
r_chiral_restr0.07
r_bond_refined_d0.008
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2917
Nucleic Acid Atoms
Solvent Atoms454
Heterogen Atoms39

Software

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