4P0D | pdb_00004p0d

The T6 backbone pilin of serotype M6 Streptococcus pyogenes has a modular three-domain structure decorated with variable loops and extensions

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4K8W	PDB Entry 4K8W

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.2	291	2.2 M NaKPO4 pH 6.4, 2 % PEG 400, 0.1 M imidazole, 20 mM Imidazole

Crystal Properties
Matthews coefficient	Solvent content
2.52	51.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 104.24	α = 90
b = 104.24	β = 90
c = 84.22	γ = 120

Symmetry
Space Group	P 63

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	110	CCD	ADSC QUANTUM 210r		2013-03-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX1	0.9537	Australian Synchrotron	MX1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.9	24.48	89.1	0.152	0.036	16.6	18.2		36565			13.3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	1.94	57.9		0.939	0.229	3.8	17.4	1592

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	PDB Entry 4K8W	1.9	50	36383	1834	88.62	0.2111	0.209	0.22	0.2499	0.25	RANDOM	22.631

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]
0.5	0.25		0.5		-1.63

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.339
r_dihedral_angle_4_deg	15.819
r_dihedral_angle_3_deg	11.817
r_dihedral_angle_1_deg	6.133
r_mcangle_it	1.831
r_angle_refined_deg	1.256
r_mcbond_it	1.12
r_mcbond_other	1.115
r_angle_other_deg	0.706
r_chiral_restr	0.074

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.339
r_dihedral_angle_4_deg	15.819
r_dihedral_angle_3_deg	11.817
r_dihedral_angle_1_deg	6.133
r_mcangle_it	1.831
r_angle_refined_deg	1.256
r_mcbond_it	1.12
r_mcbond_other	1.115
r_angle_other_deg	0.706
r_chiral_restr	0.074
r_bond_refined_d	0.008
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3472
Nucleic Acid Atoms
Solvent Atoms	441
Heterogen Atoms	4

Software

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

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.