3P3V | pdb_00003p3v

Crystal structure of a PTS dependent N-acetyl-galactosamine-IIB component (agaV, SPy_0631) from Streptococcus pyogenes at 1.65 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	277	30.00% polyethylene glycol 6000, 0.1M HEPES pH 7.0, Additive: 0.005 M Mannose, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.14	42.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.139	α = 90
b = 80.696	β = 105.26
c = 47.213	γ = 90

Symmetry
Space Group	P 1 21 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	MARMOSAIC 325 mm CCD		2010-03-11	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.96109,0.97934,0.97920	SSRL	BL9-2

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	1.65	28.638	99.3	0.059	11.6	3.7	36409	36409			20.718

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.65	1.69	99		0.491	0.491	1.6	3.6	2678

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	MAD	THROUGHOUT	1.65	28.638	36401	1816	99.32	0.1602	0.1584	0.17	0.1939	0.2	RANDOM	26.7488

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]
0.66		1.16	-0.93		0.88

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.235
r_dihedral_angle_3_deg	11.7
r_dihedral_angle_4_deg	9.895
r_scangle_it	6.759
r_dihedral_angle_1_deg	4.944
r_scbond_it	4.522
r_mcangle_it	2.931
r_mcbond_it	1.77
r_angle_refined_deg	1.55
r_angle_other_deg	0.902

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.235
r_dihedral_angle_3_deg	11.7
r_dihedral_angle_4_deg	9.895
r_scangle_it	6.759
r_dihedral_angle_1_deg	4.944
r_scbond_it	4.522
r_mcangle_it	2.931
r_mcbond_it	1.77
r_angle_refined_deg	1.55
r_angle_other_deg	0.902
r_mcbond_other	0.534
r_chiral_restr	0.092
r_bond_refined_d	0.016
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2488
Nucleic Acid Atoms
Solvent Atoms	293
Heterogen Atoms	31

Software

Software
Software Name	Purpose
SHELX	phasing
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SHELXD	phasing
autoSHARP	phasing

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.