3JQ1

Crystal structure of SusD superfamily protein (YP_001297730.1) from Bacteroides vulgatus ATCC 8482 at 1.55 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.1	277	0.2000M CaCl2, 20.0000% PEG-3350, No Buffer pH 5.1, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.28	46.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.65	α = 90
b = 94.69	β = 90
c = 165.042	γ = 90

Symmetry
Space Group	P 21 21 21

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 mirror, vertical and horizontal focussing mirrors	2009-05-08	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL12-2	0.91162,0.97956,0.97938	SSRL	BL12-2

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	1.55	29.488	98.1	0.105	0.105	8.7	3.6		146647			14.104

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	1.55	1.59	99.4		0.693	0.693	1.1	3.6	10849

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	1.55	29.488	146527	7345	97.98	0.174	0.172	0.209	RANDOM	13.866

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]
			0.15		-0.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.466
r_dihedral_angle_4_deg	19.756
r_dihedral_angle_3_deg	12.507
r_dihedral_angle_1_deg	5.796
r_scangle_it	3.475
r_scbond_it	2.278
r_angle_refined_deg	1.527
r_mcangle_it	1.432
r_angle_other_deg	0.956
r_mcbond_it	0.864

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.466
r_dihedral_angle_4_deg	19.756
r_dihedral_angle_3_deg	12.507
r_dihedral_angle_1_deg	5.796
r_scangle_it	3.475
r_scbond_it	2.278
r_angle_refined_deg	1.527
r_mcangle_it	1.432
r_angle_other_deg	0.956
r_mcbond_it	0.864
r_mcbond_other	0.277
r_chiral_restr	0.1
r_bond_refined_d	0.017
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7618
Nucleic Acid Atoms
Solvent Atoms	1475
Heterogen Atoms	38

Software

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

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.