3NOH

Crystal structure of a putative peptide binding protein (RUMGNA_00914) from Ruminococcus gnavus ATCC 29149 at 1.60 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	277	2.400000000M (NH4)2SO4, 0.1M Citrate pH 5.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
1.96	37.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.963	α = 90
b = 62.963	β = 90
c = 52.978	γ = 120

Symmetry
Space Group	P 31 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	Flat mirror (vertical focusing)	2010-06-10	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91837,0.97917,0.97874	SSRL	BL11-1

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	1.6	27.264	98.8	0.034	20.91			16202		-3	23.83

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)
	1.6	1.66	97.3		0.628	2.5

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	1.6	27.264	16192	821	98.82	0.1612	0.1596	0.1956	RANDOM	33.7307

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]
1.48	0.74		1.48		-2.22

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.887
r_dihedral_angle_4_deg	15.391
r_dihedral_angle_3_deg	12.691
r_scangle_it	6.993
r_dihedral_angle_1_deg	5.365
r_scbond_it	4.789
r_mcangle_it	3.028
r_mcbond_it	1.896
r_angle_refined_deg	1.598
r_angle_other_deg	1.016

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.887
r_dihedral_angle_4_deg	15.391
r_dihedral_angle_3_deg	12.691
r_scangle_it	6.993
r_dihedral_angle_1_deg	5.365
r_scbond_it	4.789
r_mcangle_it	3.028
r_mcbond_it	1.896
r_angle_refined_deg	1.598
r_angle_other_deg	1.016
r_mcbond_other	0.596
r_chiral_restr	0.111
r_bond_refined_d	0.017
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	953
Nucleic Acid Atoms
Solvent Atoms	109
Heterogen Atoms	11

Software

Software
Software Name	Purpose
SHELX	phasing
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	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.