Experiment: 3DV5

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3DV1	PDB entry 3DV1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1				1.0M Ammonium phosphate, 0.1M Sodium citrate, VAPOR DIFFUSION, HANGING DROP, pH 5.1, temperature 292K. Protein stock was BACE 8.45 mg/mL in 10mM Tris-HCl pH 7.4, 25mM NaCl, with a 3.8-fold excess of NVP-BAV544-AA-1 added from a 50mM stock solution in DMSO (1.4% DMSO in drop). Cryo-protectant was 20% v/v 1,2-Propanediol, 80% Reservoir solution

Crystal Properties
Matthews coefficient	Solvent content
3.04	59.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.661	α = 90
b = 103.353	β = 103.72
c = 99.474	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	96	CCD	MAR CCD 165 mm		2004-04-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	0.97933	SLS	X06SA

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	2.1	100	99.5	0.068	8.5	6.3	94339	94339			33

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)
	2.1	2.18	95.7		0.402			9020

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	PDB entry 3DV1	2.1	55.23	93604	93604	9360	99.9	0.211	0.211	0.192	0.221	RANDOM	50.342

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]
-0.14		1.75	7.01		-6.87

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	25.2
c_scangle_it	4.22
c_mcangle_it	3.03
c_scbond_it	2.99
c_mcbond_it	2.02
c_angle_deg	1.4
c_improper_angle_d	0.79
c_bond_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8925
Nucleic Acid Atoms
Solvent Atoms	453
Heterogen Atoms	105

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
CNX	phasing
CNX	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 R01GM133198.