4GL6

Crystal structure of a DUF5037 family protein (RUMGNA_01148) from Ruminococcus gnavus ATCC 29149 at 2.55 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	0.08M sodium cacodylate pH 6.5, 20% glycerol, 16% polyethylene glycol 8000, 0.16M magnesium acetate, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.83	56.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 148.653	α = 90
b = 84.139	β = 98.31
c = 53.031	γ = 90

Symmetry
Space Group	C 1 2 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	CCD	MARMOSAIC 325 mm CCD	double crystal monochromator	2012-05-03	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.91162,0.97922	SSRL	BL9-2

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	2.55	45.971	99.8	0.076	12.84			21164		-3	62.923

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	2.55	2.64	100		0.739	2.1

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	2.55	45.971	21159	1088	99.72	0.1899	0.1883	0.218	RANDOM	61.0088

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]
3.91		3.53	-4.81		1.93

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.916
r_dihedral_angle_4_deg	19.905
r_dihedral_angle_3_deg	11.245
r_dihedral_angle_1_deg	3.608
r_angle_refined_deg	1.646
r_angle_other_deg	1.404
r_chiral_restr	0.098
r_bond_refined_d	0.012
r_gen_planes_refined	0.006
r_bond_other_d	0.004

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.916
r_dihedral_angle_4_deg	19.905
r_dihedral_angle_3_deg	11.245
r_dihedral_angle_1_deg	3.608
r_angle_refined_deg	1.646
r_angle_other_deg	1.404
r_chiral_restr	0.098
r_bond_refined_d	0.012
r_gen_planes_refined	0.006
r_bond_other_d	0.004
r_gen_planes_other	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3893
Nucleic Acid Atoms
Solvent Atoms	26
Heterogen Atoms	18

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.