Experiment: 8ANM

Structure of the amyloid-forming peptide LYIQWL from Tc5b, grown from water

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	Other		ideal 5 residue beta strand form the software Fragon

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	EVAPORATION, RECRYSTALLIZATION		310	Peptide was dissolved in water in 0.15 mg/ml concentration followed by pH adjustment with NaOH to pH 4.0 - 6.0. Crystals grew after incubation at 310K.

Crystal Properties
Matthews coefficient	Solvent content
1.46	15.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 9.492	α = 90
b = 21.675	β = 90
c = 23.686	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	RIGAKU HyPix-6000HE		2021-10-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU PhotonJet-R	1.54184

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	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	0.9	15.99	99.92	0.128	0.999	9.1	5.57		3952			5.24

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	0.9	0.93			0.672	0.761	2.3

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	ideal 5 residue beta strand form the software Fragon	0.9	15.99	1.35	3936	393	99.52	0.1314	0.1299	0.13	0.1451	0.1444	5.11

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	7.745
f_angle_d	1.1546
f_chiral_restr	0.1104
f_bond_d	0.009
f_plane_restr	0.0055

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	60
Nucleic Acid Atoms
Solvent Atoms	5
Heterogen Atoms

Software

Software
Software Name	Purpose
PHENIX	refinement
CrysalisPro	data reduction
CrysalisPro	data scaling
Fragon	phasing