3TXA | pdb_00003txa

Structural Analysis of Adhesive Tip pilin, GBS104 from Group B Streptococcus agalactiae

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	295	15% PEG4000, 0.1 M Tris, pH 8.0, 0.2 M lithium sulfate, 10 mM cadmium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
3.34	63.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 124.585	α = 90
b = 124.585	β = 90
c = 117.839	γ = 120

Symmetry
Space Group	P 31 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	CCD	ADSC QUANTUM 315		2011-02-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-E	0.97949	APS	24-ID-E

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.619	39.788	100	0.096	21.9	7.3		32251

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.619	2.67	99.4		0.67	2	5.9

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 3TVY	2.619	39.788	30583	1633	99.96	0.20836	0.20591	0.2	0.25552	0.24	RANDOM	56.557

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]
2.32	1.16		2.32		-3.48

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.419
r_dihedral_angle_4_deg	20.766
r_dihedral_angle_3_deg	18.569
r_dihedral_angle_1_deg	6.946
r_scangle_it	4.029
r_scbond_it	2.314
r_mcangle_it	1.684
r_angle_refined_deg	1.586
r_mcbond_it	0.89
r_chiral_restr	0.103

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.419
r_dihedral_angle_4_deg	20.766
r_dihedral_angle_3_deg	18.569
r_dihedral_angle_1_deg	6.946
r_scangle_it	4.029
r_scbond_it	2.314
r_mcangle_it	1.684
r_angle_refined_deg	1.586
r_mcbond_it	0.89
r_chiral_restr	0.103
r_bond_refined_d	0.016
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4610
Nucleic Acid Atoms
Solvent Atoms	79
Heterogen Atoms	9

Software

Software
Software Name	Purpose
ADSC	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	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.