3RTH

Structure of Bace-1 (Beta-Secretase) in Complex with 6-(2-(3,3-Dimethylbut-1-ynyl)phenyl)quinolin-2-amine


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.629320% (w/v) PEG 5000 monomethylethyl ether (MME), 200mM sodium citrate (pH 6.6) and 200mM sodium iodide, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.7755.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102.04α = 90
b = 102.04β = 90
c = 169.103γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray2007-12-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.21ALS5.0.2

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
12.75099.60.11510.98.314861
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)
12.72.81000.4756.81424

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.72014757148799.550.23230.22550.2945RANDOM49.8245
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]
0.070.030.07-0.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.245
r_dihedral_angle_3_deg17.632
r_dihedral_angle_4_deg16.102
r_dihedral_angle_1_deg6.904
r_scangle_it2.708
r_scbond_it1.579
r_angle_refined_deg1.396
r_mcangle_it1.336
r_mcbond_it0.718
r_chiral_restr0.086
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.245
r_dihedral_angle_3_deg17.632
r_dihedral_angle_4_deg16.102
r_dihedral_angle_1_deg6.904
r_scangle_it2.708
r_scbond_it1.579
r_angle_refined_deg1.396
r_mcangle_it1.336
r_mcbond_it0.718
r_chiral_restr0.086
r_bond_refined_d0.012
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2923
Nucleic Acid Atoms
Solvent Atoms26
Heterogen Atoms27

Software

Software
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
DENZOdata reduction
PHASERphasing