4TSH | pdb_00004tsh

A Novel Protein Fold Forms an Intramolecular Lock to Stabilize the Tertiary Structure of Streptococcus mutans Adhesin P1

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3QE5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	295	Crystals were routinely grown at room temperature using the hanging drop vapor diffusion method by mixing 4uL of concentrated NA1/P3C with a mother liquor solution of 24% polyethylene glycol (PEG) 4000, 150mM ammonium phosphate, at pH 7.5. Crystals formed as large plate clusters within approximately 2 weeks. Following initial crystal growth, 8uL of a solution containing 45% PEG 4000, 100mM ammonium phosphate, at pH 7.5 was added to the crystal drop to facilitate the removal of water from the crystal and improve diffraction quality by producing a more compact and ordered crystal lattice

Crystal Properties
Matthews coefficient	Solvent content
4.07	69.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 197.521	α = 90
b = 68.887	β = 96.82
c = 81.278	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	93	CCD	ADSC QUANTUM 210		2014-05-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CHESS BEAMLINE A1	0.987	CHESS	A1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2	35.85	99.8	0.09	18.5	3.8		73061

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3QE5	2	35.847	1.34	73019	1999	99.7	0.1706	0.1696	0.18	0.2075	0.21	Random selection	49.0905

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	13.428
f_angle_d	1.238
f_chiral_restr	0.053
f_bond_d	0.022
f_plane_restr	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4692
Nucleic Acid Atoms
Solvent Atoms	545
Heterogen Atoms	4

Software

Software
Software Name	Purpose
PHENIX	refinement

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.