3NQO

Crystal structure of a MarR family transcriptional regulator (CD1569) from Clostridium difficile 630 at 2.20 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.47	277	47.0000% polyethylene glycol 200, 0.1M HEPES pH 7.47, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.739	α = 90
b = 72.672	β = 90
c = 76.072	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	CCD	MARMOSAIC 325 mm CCD	Flat collimating mirror, toroid focusing mirror	2010-03-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2		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	2.2	29.672	98.8	0.059	12.61			20101		-3	42.65

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)
	2.2	2.28	93.1		0.681	1.8

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	2.2	29.672	20052	1021	99.51	0.199	0.197	0.237	RANDOM	48.924

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]
0.53			-0.82		0.29

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.217
r_dihedral_angle_3_deg	15.153
r_dihedral_angle_4_deg	14.312
r_dihedral_angle_1_deg	6.255
r_scangle_it	4.088
r_scbond_it	2.595
r_mcangle_it	1.422
r_angle_refined_deg	1.314
r_angle_other_deg	1.057
r_mcbond_it	0.755

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.217
r_dihedral_angle_3_deg	15.153
r_dihedral_angle_4_deg	14.312
r_dihedral_angle_1_deg	6.255
r_scangle_it	4.088
r_scbond_it	2.595
r_mcangle_it	1.422
r_angle_refined_deg	1.314
r_angle_other_deg	1.057
r_mcbond_it	0.755
r_mcbond_other	0.2
r_chiral_restr	0.065
r_bond_refined_d	0.017
r_gen_planes_refined	0.006
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2824
Nucleic Acid Atoms
Solvent Atoms	63
Heterogen Atoms	60

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SOLVE	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction

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.