3IXK

Potent beta-secretase 1 inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3DM6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	299	16% PEG8000, 0.1M citrate, 0.3M lithium sulphate, 0.1M sodium chloride, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 299K

Crystal Properties
Matthews coefficient	Solvent content
3.04	59.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.838	α = 90
b = 103.075	β = 103.32
c = 100.499	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		IMAGE PLATE	RIGAKU RAXIS IV		2006-09-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.5	97.59	99.7				53317			38.2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.5	2.56	100

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3DM6	2.5	40.26	53317	2849	99.7	0.232	0.229	0.282	RANDOM	38.2

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]
-0.13		-0.17	0.37		-0.32

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.703
r_dihedral_angle_4_deg	18.528
r_dihedral_angle_3_deg	16.896
r_dihedral_angle_1_deg	8.076
r_scangle_it	5.697
r_scbond_it	4.002
r_mcangle_it	2.709
r_angle_refined_deg	1.992
r_mcbond_it	1.672
r_nbtor_refined	0.335
r_symmetry_vdw_refined	0.281
r_nbd_refined	0.233
r_chiral_restr	0.146
r_xyhbond_nbd_refined	0.141
r_symmetry_hbond_refined	0.04
r_bond_refined_d	0.016
r_gen_planes_refined	0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8805
Nucleic Acid Atoms
Solvent Atoms	71
Heterogen Atoms	180

Software

Software
Software Name	Purpose
AMoRE	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling