4EI0

Crystal structure of a DUF4466 family protein (PARMER_03218) from Parabacteroides merdae ATCC 43184 at 2.00 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.6	277	5.0% Glycerol, 19.0% polyethylene glycol 4000, 19.0% 2-propanol, 0.1M sodium citrate pH 5.6, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.5	50.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.749	α = 90
b = 85.879	β = 90
c = 128.695	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	PIXEL	DECTRIS PILATUS 6M	Rhodium-coated vertical and horizontal focusing mirrors; liquid-nitrogen cooled double crystal Si(111) monochromator	2012-03-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL12-2		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	2	29.469	97.8	0.07	9.67			47406		-3	32.338

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	2	2.07	97.5		0.706	1.6

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	2	29.469	47345	2396	99.12	0.1764	0.1742	0.2161	RANDOM	51.4653

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]
0.1			1.2		-1.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.406
r_dihedral_angle_3_deg	13.759
r_dihedral_angle_4_deg	10.765
r_dihedral_angle_1_deg	6.686
r_angle_refined_deg	1.702
r_angle_other_deg	1.185
r_chiral_restr	0.104
r_bond_refined_d	0.016
r_gen_planes_refined	0.009
r_bond_other_d	0.005

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.406
r_dihedral_angle_3_deg	13.759
r_dihedral_angle_4_deg	10.765
r_dihedral_angle_1_deg	6.686
r_angle_refined_deg	1.702
r_angle_other_deg	1.185
r_chiral_restr	0.104
r_bond_refined_d	0.016
r_gen_planes_refined	0.009
r_bond_other_d	0.005
r_gen_planes_other	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4641
Nucleic Acid Atoms
Solvent Atoms	355
Heterogen Atoms	6

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

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.