3K0Y

Crystal structure of Putative TOXIN related protein (YP_001303978.1) from Parabacteroides distasonis ATCC 8503 at 2.16 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.79	277	5.0000% polyethylene glycol 3000, 44.0000% polyethylene glycol 400, 0.1M MES pH 5.79, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K, VAPOR DIFFUSION, SITTING DROP

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.722	α = 90
b = 71.722	β = 90
c = 102.566	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	MARMOSAIC 325 mm CCD	Flat collimating mirror, toroid focusing mirror	2009-07-31	M	MAD
2	1	x-ray	100	CCD	MARMOSAIC 325 mm CCD	Flat mirror (vertical focusing)	2009-02-23	M	MAD
,0.91162	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.97911	SSRL	BL9-2
2	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.97835,0.97876	SSRL	BL11-1
,0.91162

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	2.16	39.559	99.4	0.032	19.28			16892		-3	52.236

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1,2	2.16	2.24	99.5		0.688	1.8

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	2.16	39.559	16861	853	99.85	0.205	0.203	0.235	RANDOM	50.118

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]
-1.48	-0.74		-1.48		2.21

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.016
r_dihedral_angle_4_deg	17.405
r_dihedral_angle_3_deg	15.148
r_dihedral_angle_1_deg	6.504
r_scangle_it	3.529
r_scbond_it	2.241
r_mcangle_it	1.678
r_angle_refined_deg	1.596
r_mcbond_it	0.922
r_angle_other_deg	0.85

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.016
r_dihedral_angle_4_deg	17.405
r_dihedral_angle_3_deg	15.148
r_dihedral_angle_1_deg	6.504
r_scangle_it	3.529
r_scbond_it	2.241
r_mcangle_it	1.678
r_angle_refined_deg	1.596
r_mcbond_it	0.922
r_angle_other_deg	0.85
r_mcbond_other	0.21
r_chiral_restr	0.098
r_bond_refined_d	0.018
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	1580
Nucleic Acid Atoms
Solvent Atoms	56
Heterogen Atoms	23

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHARP	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 R01GM133198.