3MSL

Fragment Based Discovery and Optimisation of BACE-1 Inhibitors

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		6.6	273	20% PEG 5000MME 180mM Ammonium Iodide and 180mM Sodium Citrate pH6.6 , VAPOR DIFFUSION, HANGING DROP, temperature 273K

Crystal Properties
Matthews coefficient	Solvent content
2.76	55.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.19	α = 90
b = 100.19	β = 90
c = 172.84	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 QUANTUM 315r		2008-09-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04		Diamond	I04

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	2.4	61.2	86.3	0.102	0.106	12.9	11.89		17067		2	40.5

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	2.4	2.46	89.5		0.287	0.131	4.3	11.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	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	2.4	50.1	2	17938	17067	870	86.4	0.228	0.228	0.235	RANDOM	24.11

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]
-0.72	-0.36		-0.72		1.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.79
r_dihedral_angle_4_deg	14.17
r_dihedral_angle_3_deg	13.727
r_dihedral_angle_1_deg	5.434
r_angle_refined_deg	1.036
r_mcangle_it	0.59
r_scangle_it	0.332
r_mcbond_it	0.328
r_scbond_it	0.184
r_chiral_restr	0.068
r_bond_refined_d	0.006
r_gen_planes_refined	0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
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	2965
Nucleic Acid Atoms
Solvent Atoms	159
Heterogen Atoms	27

Software

Software
Software Name	Purpose
DNA	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling