4DSD

Crystal structure of a putative periplasmic protein (BACOVA_05534) from Bacteroides ovatus ATCC 8483 at 1.75 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	293	5.0% polyethylene glycol 6000, 0.1M citric acid pH 5.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.07	59.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 107.381	α = 90
b = 107.381	β = 90
c = 63.01	γ = 90

Symmetry
Space Group	P 42 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	Vertical focusing mirror; double crystal Si(111) monochromator	2012-02-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL14-1		SSRL	BL14-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	29.892	99.9	0.081	11.8	7.2	37675	37675

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	100		0.689	0.689	1.1	7.2	2734

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	SAD	THROUGHOUT	1.75	29.892	37622	1881	99.84	0.1793	0.1774	0.2145	RANDOM	39.2453

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]
-0.05			-0.05		0.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.039
r_dihedral_angle_4_deg	22.092
r_dihedral_angle_3_deg	12.874
r_dihedral_angle_1_deg	5.885
r_angle_refined_deg	1.593
r_angle_other_deg	0.938
r_chiral_restr	0.1
r_bond_refined_d	0.015
r_gen_planes_refined	0.007
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.039
r_dihedral_angle_4_deg	22.092
r_dihedral_angle_3_deg	12.874
r_dihedral_angle_1_deg	5.885
r_angle_refined_deg	1.593
r_angle_other_deg	0.938
r_chiral_restr	0.1
r_bond_refined_d	0.015
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	1998
Nucleic Acid Atoms
Solvent Atoms	247
Heterogen Atoms	32

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.