3CLO | pdb_00003clo

Crystal structure of putative transcriptional regulator containing a LuxR DNA binding domain (NP_811094.1) from Bacteroides thetaiotaomicron VPI-5482 at 2.04 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	277	NANODROP, 4.3M NaCl, 0.1M HEPES pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.64	66.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 233.65	α = 90
b = 233.65	β = 90
c = 125.273	γ = 120

Symmetry
Space Group	H 3 2

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	2008-01-12	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.91162, 0.97964	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	2.04	48.45	100	0.095	10.2	5.63		82770		-3	36.169

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	2.04	2.11	100		0.998	1.83	5.66

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-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	2.04	48.45	82770	4142	99.97	0.189	0.187	0.19	0.217	0.22	RANDOM	35.323

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]
-0.98	-0.49		-0.98		1.46

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.327
r_dihedral_angle_4_deg	14.475
r_dihedral_angle_3_deg	12.476
r_scangle_it	6.759
r_scbond_it	4.556
r_dihedral_angle_1_deg	4.013
r_mcangle_it	2.503
r_angle_refined_deg	1.301
r_mcbond_it	1.264
r_angle_other_deg	0.891
r_mcbond_other	0.686
r_symmetry_vdw_other	0.244
r_nbd_refined	0.2
r_nbd_other	0.192
r_symmetry_hbond_refined	0.192
r_symmetry_vdw_refined	0.186
r_metal_ion_refined	0.169
r_xyhbond_nbd_refined	0.166
r_nbtor_refined	0.165
r_nbtor_other	0.081
r_chiral_restr	0.078
r_bond_refined_d	0.012
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6120
Nucleic Acid Atoms
Solvent Atoms	494
Heterogen Atoms	15

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing