3JYS

Crystal structure of SusD superfamily protein (YP_001298690.1) from Bacteroides vulgatus ATCC 8482 at 2.00 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.8	277	0.2000M MgCl2, 20.0000% PEG-3350, No Buffer pH 5.8, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.4	48.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.929	α = 90
b = 63.929	β = 90
c = 266.398	γ = 90

Symmetry
Space Group	P 41 21 2

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	2009-05-15	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.91162,0.97936	SSRL	BL9-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	29.111	100	0.075	0.075	16.8	7.1		38690			32.57

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	2	2.05	100		0.643	0.643	1.2	7.3	2786

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	29.111	38586	1931	99.93	0.179	0.178	0.198	RANDOM	32.083

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]
1.33			1.33		-2.66

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.632
r_dihedral_angle_3_deg	14.618
r_dihedral_angle_4_deg	8.307
r_dihedral_angle_1_deg	6.145
r_scangle_it	3.059
r_scbond_it	2.046
r_angle_refined_deg	1.476
r_mcangle_it	1.25
r_angle_other_deg	0.967
r_mcbond_it	0.724

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.632
r_dihedral_angle_3_deg	14.618
r_dihedral_angle_4_deg	8.307
r_dihedral_angle_1_deg	6.145
r_scangle_it	3.059
r_scbond_it	2.046
r_angle_refined_deg	1.476
r_mcangle_it	1.25
r_angle_other_deg	0.967
r_mcbond_it	0.724
r_mcbond_other	0.198
r_chiral_restr	0.093
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	3814
Nucleic Acid Atoms
Solvent Atoms	266
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction

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.