2VA6

X-ray crystal structure of beta secretase complexed with compound 24

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1W50	PDB ENTRY 1W50

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1				20-22.5% (W/V) PEG 5000 MONOMETHYLETHYL (MME), 200 MM SODIUM CITRATE (PH 6.6) AND 200 MM AMMONIUM IODIDE

Crystal Properties
Matthews coefficient	Solvent content
3.06	59.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 102.971	α = 90
b = 102.971	β = 90
c = 167.28	γ = 120

Symmetry
Space Group	P 61 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC CCD			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2		ESRF	ID14-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.5	47	99.9	0.07		2.5		17850

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.56	100		0.4

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	PDB ENTRY 1W50	2.5	47.28	17805	964	99.8	0.228	0.224	0.289	RANDOM	39.45

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.808
r_dihedral_angle_4_deg	16.734
r_dihedral_angle_3_deg	16.191
r_dihedral_angle_1_deg	8.205
r_angle_refined_deg	1.48
r_angle_other_deg	0.903
r_symmetry_vdw_other	0.222
r_nbd_refined	0.217
r_nbd_other	0.21
r_nbtor_refined	0.191
r_symmetry_vdw_refined	0.178
r_xyhbond_nbd_refined	0.144
r_scangle_it	0.095
r_nbtor_other	0.09
r_chiral_restr	0.088
r_mcangle_it	0.076
r_scbond_it	0.072
r_symmetry_hbond_refined	0.067
r_mcbond_it	0.051
r_bond_refined_d	0.013
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2961
Nucleic Acid Atoms
Solvent Atoms	88
Heterogen Atoms	27

Software

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