6JT4 | pdb_00006jt4

Crystal Structure of BACE1 in complex with N-{3-[(4S,6S)-2-amino-4-methyl-6-(trifluoromethyl)-5,6-dihydro-4H-1,3-thiazin-4-yl]-4-fluorophenyl}-5-(fluoromethoxy)pyrazine-2-carboxamide

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293.15	0.2 M sodium citrate tribasic pH 6.5, 0.2 M ammonium iodide, 20.5% w/v PEG 5000MME

Crystal Properties
Matthews coefficient	Solvent content
2.73	59.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 101.59	α = 90
b = 101.59	β = 90
c = 170.351	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	IMAGE PLATE	RIGAKU RAXIS IV++		2015-12-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.54178

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	2.2	56.78	99.9	0.09	0.096	0.033	0.998	7.8	8		27088

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.27	99.6		0.448	0.478	0.165	0.924		8.1

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1W50	2.2	20	25639	1407	99.82	0.1972	0.1951	0.2	0.2339	0.24	RANDOM	31.602

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	35.544
r_dihedral_angle_4_deg	14.744
r_dihedral_angle_3_deg	13.999
r_dihedral_angle_1_deg	6.747
r_angle_refined_deg	1.329
r_angle_other_deg	0.762
r_chiral_restr	0.253
r_bond_refined_d	0.01
r_gen_planes_refined	0.005
r_bond_other_d	0.003

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.544
r_dihedral_angle_4_deg	14.744
r_dihedral_angle_3_deg	13.999
r_dihedral_angle_1_deg	6.747
r_angle_refined_deg	1.329
r_angle_other_deg	0.762
r_chiral_restr	0.253
r_bond_refined_d	0.01
r_gen_planes_refined	0.005
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2862
Nucleic Acid Atoms
Solvent Atoms	204
Heterogen Atoms	46

Software

Software
Software Name	Purpose
Aimless	data extraction
MOSFLM	data processing
MOLREP	phasing
REFMAC	refinement

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.