4MRU

Crystal structure of a susD homolog (BT1281) from Bacteroides thetaiotaomicron VPI-5482 at 1.90 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	277	0.2000M magnesium acetate, 20.0000% polyethylene glycol 8000, 0.1M sodium cacodylate pH 6.5, NANODROP', VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.37	48.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.146	α = 78.73
b = 74.673	β = 73.51
c = 78.057	γ = 78.62

Symmetry
Space Group	P 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	PIXEL	DECTRIS PILATUS 6M	Rhodium-coated vertical and horizontal focusing mirrors; liquid-nitrogen cooled double crystal Si(111) monochromator	2013-07-16	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL12-2	0.9794,0.9184,0.9793	SSRL	BL12-2

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	1.9	28.387	84.9	0.075	5.07	2.4		74269		-3	23.939

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	1.9	1.97	74.6		0.239	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	1.9	28.387	74269	3702	87.63	0.1369	0.1348	0.1757	RANDOM	25.2532

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]
-0.73	-0.14	0.58	1.38	-0.39	-0.56

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.69
r_dihedral_angle_4_deg	16.68
r_dihedral_angle_3_deg	12.173
r_dihedral_angle_1_deg	5.911
r_mcangle_it	3.065
r_mcbond_it	2.372
r_mcbond_other	2.369
r_angle_refined_deg	1.517
r_angle_other_deg	0.962
r_chiral_restr	0.049

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.69
r_dihedral_angle_4_deg	16.68
r_dihedral_angle_3_deg	12.173
r_dihedral_angle_1_deg	5.911
r_mcangle_it	3.065
r_mcbond_it	2.372
r_mcbond_other	2.369
r_angle_refined_deg	1.517
r_angle_other_deg	0.962
r_chiral_restr	0.049
r_bond_refined_d	0.013
r_gen_planes_refined	0.009
r_bond_other_d	0.004
r_gen_planes_other	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7566
Nucleic Acid Atoms
Solvent Atoms	859
Heterogen Atoms	70

Software

Software
Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
XSCALE	data scaling
REFMAC	refinement
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.