Experiment: 4Y6K

Complex structure of presenilin homologue PSH bound to an inhibitor

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4HYG

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		291	0.1 M Glycine pH 3.6, 0.2 M (NH4)2SO4, 20% (w/v) PEG500MME, 6% (w/v) Glycerol, 0.04% (w/v) Anapoe-C12E8,1% (w/v) N-heptyl-b-D-thioglucoside

Crystal Properties
Matthews coefficient	Solvent content
3.92	68.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 168.617	α = 90
b = 201.691	β = 90
c = 117.505	γ = 90

Symmetry
Space Group	C 2 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	100	CCD	RIGAKU SATURN 724		2013-11-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU	1.0	SPring-8	BL41XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	3.85	50	51	8.9	6.5		7729

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	4HYG	3.855	48.203	1.69	7725	361	40.03	0.3222	0.3199	0.3337	0.3675	0.3787

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	19.268
f_angle_d	1.495
f_chiral_restr	0.058
f_plane_restr	0.011
f_bond_d	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7102
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	98

Software

Software
Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling