3RTM | pdb_00003rtm

Structure of Bace-1 (Beta-Secretase) in Complex with 3-(2-Aminoquinolin-3-yl)-N-cyclohexyl-N-methylpropanamide

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.6	293	20% (w/v) PEG 5000 monomethylethyl ether (MME), 200mM sodium citrate (pH 6.6) and 200mM sodium iodide, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.77	55.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 101.875	α = 90
b = 101.875	β = 90
c = 169.165	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					2008-02-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.2	1	ALS	5.0.2

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	2.75	20	98.5	0.082	12.5	7.6		13736

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	2.75	2.85	97.5		0.387		5.7	1308

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.76	20	13653	680	98.05	0.2246	0.2212	0.2175	0.2884	0.219	RANDOM	54.768

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]
1.45	0.73		1.45		-2.18

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.714
r_dihedral_angle_3_deg	18.435
r_dihedral_angle_4_deg	16.039
r_dihedral_angle_1_deg	7.047
r_scangle_it	2.851
r_scbond_it	1.667
r_angle_refined_deg	1.455
r_mcangle_it	1.399
r_mcbond_it	0.751
r_chiral_restr	0.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.714
r_dihedral_angle_3_deg	18.435
r_dihedral_angle_4_deg	16.039
r_dihedral_angle_1_deg	7.047
r_scangle_it	2.851
r_scbond_it	1.667
r_angle_refined_deg	1.455
r_mcangle_it	1.399
r_mcbond_it	0.751
r_chiral_restr	0.09
r_bond_refined_d	0.013
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2910
Nucleic Acid Atoms
Solvent Atoms	54
Heterogen Atoms	38

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
PHASER	phasing

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.