3UFL

Discovery of Pyrrolidine-based b-Secretase Inhibitors: Lead Advancement through Conformational Design for Maintenance of Ligand Binding Efficiency

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	273	pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 273K

Crystal Properties
Matthews coefficient	Solvent content
2.99	58.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 103.668	α = 90
b = 127.642	β = 90
c = 76.846	γ = 90

Symmetry
Space Group	C 2 2 21

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 210		2007-11-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-ID	1.0	APS	17-ID

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	1.9	50	98.9	0.072	10.1	6.6	40327	39870	1	1

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	1.9	1.97	92		0.457		4.5	3675

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.9	31.91	40327	39826	2038	98.72	0.2139	0.2139	0.2122	0.2454	RANDOM	29.8936

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]
-0.23			0.44		-0.21

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.672
r_dihedral_angle_4_deg	16.676
r_dihedral_angle_3_deg	12.86
r_dihedral_angle_1_deg	6.28
r_scangle_it	1.979
r_angle_refined_deg	1.158
r_scbond_it	1.158
r_mcangle_it	1.097
r_mcbond_it	0.617
r_nbtor_refined	0.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.672
r_dihedral_angle_4_deg	16.676
r_dihedral_angle_3_deg	12.86
r_dihedral_angle_1_deg	6.28
r_scangle_it	1.979
r_angle_refined_deg	1.158
r_scbond_it	1.158
r_mcangle_it	1.097
r_mcbond_it	0.617
r_nbtor_refined	0.31
r_symmetry_vdw_refined	0.237
r_nbd_refined	0.186
r_symmetry_hbond_refined	0.152
r_xyhbond_nbd_refined	0.123
r_chiral_restr	0.089
r_bond_refined_d	0.008
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2927
Nucleic Acid Atoms
Solvent Atoms	308
Heterogen Atoms	66

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
MOLREP	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.