3CU5

Crystal structure of a two component transcriptional regulator AraC from Clostridium phytofermentans ISDg

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	294	1.8 M Tri-ammonium citrate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.326	α = 90
b = 87.038	β = 106.22
c = 52.697	γ = 90

Symmetry
Space Group	P 1 21 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	MAR CCD 165 mm		2008-04-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.97980	APS	31-ID

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	2.5	50	85.8	0.101	7.7	3.3		16975

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	2.5	2.59	36.4		0.407		1.4	727

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	2.6	20	8565	395	100	0.189	0.183	0.3	RANDOM	22.484

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]
-0.94		0.82	0.16		1.24

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	43.38
r_dihedral_angle_4_deg	30.959
r_dihedral_angle_3_deg	22.906
r_scbond_it	14.252
r_dihedral_angle_1_deg	10.749
r_mcangle_it	5.854
r_angle_refined_deg	2.098
r_mcbond_it	1.227
r_scangle_it	1.061
r_chiral_restr	0.128

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	43.38
r_dihedral_angle_4_deg	30.959
r_dihedral_angle_3_deg	22.906
r_scbond_it	14.252
r_dihedral_angle_1_deg	10.749
r_mcangle_it	5.854
r_angle_refined_deg	2.098
r_mcbond_it	1.227
r_scangle_it	1.061
r_chiral_restr	0.128
r_bond_refined_d	0.018
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2020
Nucleic Acid Atoms
Solvent Atoms	95
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHELX	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
HKL-2000	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.