3CWR | pdb_00003cwr

Crystal structure of transcriptional regulator of TetR family (YP_425770.1) from Rhodospirillum rubrum ATCC 11170 at 1.50 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.79	293	NANODROP, 1.27M Ammonium sulfate, 0.1M MES pH 5.79, VAPOR DIFFUSION, SITTING DROP, temperature 293K
2	VAPOR DIFFUSION, SITTING DROP	5.64	293	NANODROP, 1.18M Ammonium sulfate, 0.1M MES pH 5.64, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.34	α = 90
b = 53.34	β = 90
c = 234.24	γ = 120

Symmetry
Space Group	P 65

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)	2008-04-03	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	ADSC QUANTUM 315	1m long Rh coated bent cylindrical mirror for horizontal and vertical focusing	2008-03-23	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.97852	SSRL	BL11-1
2	SYNCHROTRON	SSRL BEAMLINE BL1-5	0.979137, 0.918381, 0.978532	SSRL	BL1-5

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	1.5	29.285	98.3	0.036	17.05			59433		-3	20.454

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)
	1.5	1.55	95.3		0.366	2.3

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	1.5	29.285	59383	3001	98.97	0.151	0.149	0.16	0.186	0.19	RANDOM	19.055

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]
0.79	0.39		0.79		-1.18

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.856
r_dihedral_angle_4_deg	17.683
r_dihedral_angle_3_deg	11.279
r_sphericity_free	7.645
r_scangle_it	6.71
r_scbond_it	5.159
r_sphericity_bonded	4.397
r_dihedral_angle_1_deg	3.342
r_mcangle_it	3.275
r_rigid_bond_restr	2.944

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2926
Nucleic Acid Atoms
Solvent Atoms	327
Heterogen Atoms	24

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.