3DXD

Crystal structure of the intracellular domain of human APP (T668E mutant) in complex with Fe65-PTB2

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	4.6	293	3.2 M NaCl, 0.1 M sodium acetate , pH 4.6, VAPOR DIFFUSION, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.72	66.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 115.115	α = 90
b = 115.115	β = 90
c = 75.254	γ = 120

Symmetry
Space Group	P 61

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	ADSC QUANTUM 4		2008-07-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2	0.933	ESRF	ID14-2

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	2.2	60	99.7	0.062	30.3	10.6		28638

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	2.2	2.32	97.9		0.432	3.9	7.3

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION		THROUGHOUT	2.2	37.69	28638	1464	99.32	0.204	0.202	0.247	RANDOM	50.925

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]
-0.04	-0.02		-0.04		0.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.767
r_dihedral_angle_3_deg	17.04
r_dihedral_angle_4_deg	14.765
r_dihedral_angle_1_deg	6.74
r_scangle_it	3.732
r_scbond_it	2.624
r_mcangle_it	1.898
r_angle_refined_deg	1.4
r_mcbond_it	1.27
r_nbtor_refined	0.299

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.767
r_dihedral_angle_3_deg	17.04
r_dihedral_angle_4_deg	14.765
r_dihedral_angle_1_deg	6.74
r_scangle_it	3.732
r_scbond_it	2.624
r_mcangle_it	1.898
r_angle_refined_deg	1.4
r_mcbond_it	1.27
r_nbtor_refined	0.299
r_nbd_refined	0.212
r_symmetry_hbond_refined	0.204
r_symmetry_vdw_refined	0.183
r_xyhbond_nbd_refined	0.177
r_chiral_restr	0.097
r_bond_refined_d	0.015
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2403
Nucleic Acid Atoms
Solvent Atoms	128
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
DNA	data collection
MOSFLM	data reduction
SCALA	data scaling
SOLVE	phasing

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.