5BS6 | pdb_00005bs6

Apo structure of transcriptional factor AraR from Bacteroides thetaiotaomicron VPI

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.2	289	0.4 M sodium di-hydrogen phosphate/1.6M di-potassium hydrogen phosphate, 0.2 M sodum chloride, 0.1 M Tris

Crystal Properties
Matthews coefficient	Solvent content
3.42	64.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 176.437	α = 90
b = 176.437	β = 90
c = 118.426	γ = 120

Symmetry
Space Group	H 3

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	ADSC QUANTUM 315		2005-10-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.9794	APS	19-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	2.35	50	99.7	0.117	9.6	3.7		56682

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	2.35	2.39	98.1		0.831		3.4	2767

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 (Depositor)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	FREE R-VALUE	2.35	41.38	49428	2641	91.31	0.1973	0.1954	0.233	0.2384	RANDOM	38.864

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]
-0.57	-0.57		-0.57		1.86

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.052
r_dihedral_angle_4_deg	12.975
r_dihedral_angle_3_deg	12.707
r_dihedral_angle_1_deg	5.918
r_angle_refined_deg	1.231
r_angle_other_deg	0.685
r_chiral_restr	0.067
r_bond_refined_d	0.009
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7213
Nucleic Acid Atoms
Solvent Atoms	259
Heterogen Atoms	16

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-3000	phasing
SBC-Collect	data collection