1YWM | pdb_00001ywm

Crystal structure of the N-terminal domain of group B Streptococcus alpha C protein

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		ALPHA C SELENOMETHIONYL MUTANT (2 SELENIUM ATOMS)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	294	sodium acetate, PEG4000, DTT, pH 4.60, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.88	57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.464	α = 90
b = 56.464	β = 90
c = 271.617	γ = 120

Symmetry
Space Group	P 61 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	77	CCD	SBC-2		2000-12-15	M	SINGLE WAVELENGTH
2	1	x-ray		CCD	ADSC QUANTUM 4		2004-06-15	M	SINGLE WAVELENGTH
1,2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID		APS	19-ID
2	SYNCHROTRON	NSLS BEAMLINE X26C		NSLS	X26C

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	1.86	40	95.1	0.053	29.88	14		19465

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	1.86	1.93	71.7		0.339	4.69

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	SAD	THROUGHOUT	ALPHA C SELENOMETHIONYL MUTANT (2 SELENIUM ATOMS)	1.86	39.53	19465	19465	2193	99.8	0.193	0.193	0.188	0.19	0.233	0.23	RANDOM	23.69

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]
0.09	0.04		0.09		-0.13

RMS Deviations
Key	Refinement Restraint Deviation
r_scangle_it	9.687
r_scbond_it	7.814
r_mcangle_it	5.16
r_dihedral_angle_1_deg	5.015
r_mcbond_it	3.332
r_angle_refined_deg	1.406
r_symmetry_vdw_refined	0.226
r_nbd_refined	0.198
r_symmetry_hbond_refined	0.152
r_xyhbond_nbd_refined	0.148

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1409
Nucleic Acid Atoms
Solvent Atoms	222
Heterogen Atoms	20

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
EPMR	phasing
REFMAC	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.