6G8D | pdb_00006g8d

Crystal Structure of the Amyloid-like LNIYQY segment from the R1 repeat of the E. coli Biofilm-associated CsgA Curli protein

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	Other		Ideal beta-strand

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	Reservoir contained 0.1 M HEPES pH 7.5, 20% v/v Jeffamine M-600, 10 mM of the TAIVVQ peptide

Crystal Properties
Matthews coefficient	Solvent content
1.35	8.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.18	α = 90
b = 4.82	β = 126.01
c = 26.69	γ = 90

Symmetry
Space Group	C 1 2 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	PIXEL	DECTRIS PILATUS 6M-F		2016-05-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)	0.9763	PETRA III, EMBL c/o DESY	P14 (MX2)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.85	13.32	96	0.189	0.225	0.975	3.46	3.506		462			23.727

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.85	2.07	98.4		0.463	0.529	0.891	2.31	4.181

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	Ideal beta-strand	1.85	13.32	415	46	97.26	0.178	0.1764	0.19	0.191	0.22	RANDOM	24.728

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]
-0.49		1.07	-2.49		0.7

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.579
r_dihedral_angle_3_deg	8.709
r_dihedral_angle_1_deg	3.04
r_angle_refined_deg	1.506
r_angle_other_deg	1.09
r_chiral_restr	0.092
r_bond_other_d	0.041
r_bond_refined_d	0.023
r_gen_planes_refined	0.009
r_gen_planes_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	58
Nucleic Acid Atoms
Solvent Atoms	1
Heterogen Atoms

Software

Software
Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

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 R01GM157729.