6FHC | pdb_00006fhc

Crystal Structure of the Amyloid-like hexametric polymorph of the LFKFFK segment from the S. aureus PSMalpha3

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	Other		Ideal Beta-strand of poly-alanine

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	Reservoir contained 0.2M potassium thiocyanate, 20% Polyethylene glycol 3350

Crystal Properties
Matthews coefficient	Solvent content
2.14	42.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 35.791	α = 90
b = 35.791	β = 90
c = 9.632	γ = 120

Symmetry
Space Group	P 65

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 2M		2014-07-24	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)	Rpim I (All)	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	1.5	100	97.4	0.126	0.131	0.034	5.4	13.8		1179

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.5	1.55	98.3		0.787	0.831	0.258	0.871		9.6

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 of poly-alanine	1.51	31	1057	121	97.76	0.1224	0.1176	0.12	0.1623	0.16	RANDOM	13.433

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]
0.08	0.04		0.08		-0.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	19.639
r_sphericity_bonded	9.746
r_dihedral_angle_1_deg	8.623
r_dihedral_angle_3_deg	7.158
r_rigid_bond_restr	2.057
r_angle_refined_deg	1.995
r_angle_other_deg	1.143
r_chiral_restr	0.084
r_bond_refined_d	0.016
r_gen_planes_refined	0.008

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	19.639
r_sphericity_bonded	9.746
r_dihedral_angle_1_deg	8.623
r_dihedral_angle_3_deg	7.158
r_rigid_bond_restr	2.057
r_angle_refined_deg	1.995
r_angle_other_deg	1.143
r_chiral_restr	0.084
r_bond_refined_d	0.016
r_gen_planes_refined	0.008
r_bond_other_d	0.004
r_gen_planes_other	0.001
r_sphericity_free

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	60
Nucleic Acid Atoms
Solvent Atoms	5
Heterogen Atoms	21

Software

Software
Software Name	Purpose
XDS	data reduction
SCALEPACK	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.