2B8L | pdb_00002b8l

Crystal structure of human beta secretase complexed with inhibitor

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	1.5M LITHIUM SULFATE, 0.1M HEPES BUFFER, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.82	56.42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 104.678	α = 90
b = 127.917	β = 90
c = 76.122	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	193	IMAGE PLATE	RIGAKU RAXIS IV			M	SINGLE WAVELENGTH

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	1.7	50	94.8	0.067	17.8	3.5		53390			25.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	PDB entry 1TFQ	1.7	6	55011	49022	4986	89	0.23	0.22	0.252	RANDOM	27.3

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]
-2.72			8.27		-5.55

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	25.7
c_angle_deg	1.4
c_improper_angle_d	0.82
c_bond_d	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2979
Nucleic Acid Atoms
Solvent Atoms	201
Heterogen Atoms	41

Software

Software
Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
CNX	refinement
HKL-2000	data reduction
CNX	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.