Experiment: 3K5D

Crystal Structure of BACE-1 in complex with AHM178

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	292	Crystals were grown from 12% (w/v) PEG 8,000, 0.1M KCl, 5% glycerol. Protein stock was 12.7mg/ml BACE in 10mM Tris-HCl pH 7.4, 25mM NaCl, with a 2-fold excess of compound added from a 50mM stock solution in DMSO (0.55% DMSO in drop). Before mounting, the crystals were briefly transferred to a cryo-protectant solution containing 12% (w/v) PEG 8,000, 0.5M KCl, 15% glycerol., VAPOR DIFFUSION, HANGING DROP, temperature 292K

Crystal Properties
Matthews coefficient	Solvent content
3.04	59.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.547	α = 90
b = 101.299	β = 104.16
c = 102.218	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	105	CCD	MAR CCD 165 mm	mirrors	2002-06-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	0.98030	SLS	X06SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.9	80	100	0.109	0.109	7.6	7.1	36242	36226			67.4

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.9	3	100		0.48	0.48

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	2.9	71.39	36242	36217	3615	99.5	0.205	0.204	0.202	0.1963	0.238	0.2335	RANDOM	50.6

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]
-6.85		2.26	4.32		2.52

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	25.1
c_scangle_it	8.08
c_scbond_it	5.63
c_mcangle_it	5.61
c_mcbond_it	3.58
c_angle_deg	0.8
c_improper_angle_d	0.7
c_bond_d	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8867
Nucleic Acid Atoms
Solvent Atoms	71
Heterogen Atoms	111

Software

Software
Software Name	Purpose
CNX	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNX	phasing