6G8E | pdb_00006g8e

Crystal Structure of the Amyloid-like VTQVGF segment from the R5 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 3.0 M Sodium chloride and 0.1 M BIS-Tris pH 5.5

Crystal Properties
Matthews coefficient	Solvent content
1.42	13.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 4.81	α = 65.82
b = 19.34	β = 83.72
c = 21.9	γ = 83.2

Symmetry
Space Group	P 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 PILATUS3 2M		2015-09-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.8729	ESRF	ID23-2

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	1.7	19.93	98.4	0.275	0.298	0.979	5.02	6.923		776			16.637

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	1.7	1.82	99.3		0.442	0.481	0.904	3.18	6.522

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	1.7	19.93	698	78	98.98	0.1235	0.1226	0.14	0.132	0.15	RANDOM	9.47

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]
0.89	0.03	0.14	-0.2	-0.36	-0.58

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.365
r_dihedral_angle_3_deg	5.056
r_dihedral_angle_1_deg	2.84
r_angle_refined_deg	1.529
r_angle_other_deg	0.861
r_chiral_restr	0.069
r_bond_other_d	0.021
r_bond_refined_d	0.017
r_gen_planes_refined	0.007
r_gen_planes_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	92
Nucleic Acid Atoms
Solvent Atoms	6
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.