4D8C

Crystal Structure of Human Beta Secretase in Complex with NVP-BXD552, derived from a co-crystallization experiment

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	292	1.0M ammonium sulfate in water, pH 5.5, vapor diffusion, hanging drop, temperature 292K

Crystal Properties
Matthews coefficient	Solvent content
3.08	60.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.133	α = 90
b = 103.505	β = 103.98
c = 100.409	γ = 90

Symmetry
Space Group	P 1 21 1

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	MARMOSAIC 225 mm CCD	mirrors	2008-01-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	1.00161	SLS	X10SA

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	2.07	71.05	99.8	0.058	14.41	4.6	99152	99152		-3	40.235

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	2.07	2.14	99.9		0.339	4.36	4.64	9371

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	FOURIER SYNTHESIS	THROUGHOUT	2.07	70.95	99152	99152	9956	99.8	0.193	0.193	0.191	0.211	RANDOM	40.5968

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]
-3.96		-0.03	9.8		-5.84

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	25.8
c_scangle_it	2.97
c_mcangle_it	2.43
c_scbond_it	1.95
c_mcbond_it	1.48
c_angle_deg	0.9
c_improper_angle_d	0.66
c_bond_d	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8925
Nucleic Acid Atoms
Solvent Atoms	704
Heterogen Atoms	130

Software

Software
Software Name	Purpose
XSCALE	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
CNX	phasing
CNX	refinement

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.