3S9J

Crystal structure of a member of duf4221 family (BVU_1028) from Bacteroides vulgatus atcc 8482 at 1.75 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	10.00% Glycerol, 3.60M sodium formate, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.31	62.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 113.551	α = 90
b = 113.551	β = 90
c = 77.697	γ = 120

Symmetry
Space Group	P 63

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	double crystal monochromator	2011-04-22	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.91162,0.97925	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	1.75	28.388	99.9	0.078	0.078	10.5	4.5	57440	57440			24.618

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	1.75	1.8	99.9		0.595	0.595	1.3	4.4	4188

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	1.75	28.388	57423	2913	99.95	0.1436	0.1423	0.1686	RANDOM	33.9517

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]
0.7	0.35		0.7		-1.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.288
r_dihedral_angle_3_deg	14.253
r_dihedral_angle_4_deg	14.049
r_dihedral_angle_1_deg	6.407
r_scangle_it	6.122
r_scbond_it	4.118
r_mcangle_it	2.648
r_mcbond_it	1.605
r_angle_refined_deg	1.475
r_angle_other_deg	0.892

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.288
r_dihedral_angle_3_deg	14.253
r_dihedral_angle_4_deg	14.049
r_dihedral_angle_1_deg	6.407
r_scangle_it	6.122
r_scbond_it	4.118
r_mcangle_it	2.648
r_mcbond_it	1.605
r_angle_refined_deg	1.475
r_angle_other_deg	0.892
r_mcbond_other	0.458
r_chiral_restr	0.091
r_bond_refined_d	0.015
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3003
Nucleic Acid Atoms
Solvent Atoms	468
Heterogen Atoms	60

Software

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