3BRU | pdb_00003bru

Crystal structure of regulatory protein TetR from Rhodobacter sphaeroides

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	291	20% PEG 3000, 0.1 M HEPES buffer, 0.2 M Sodium chloride, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.39	48.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.416	α = 90
b = 82.564	β = 90
c = 91.316	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	ADSC QUANTUM 315		2007-11-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97920	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	2.3	40	99.3	0.183	6.3	11.5	21647	21647			48.3

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	2.3	2.38	96.7		0.67	1.95	6.5	2068

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.3	40	21442	21442	1100	98.38	0.1702	0.1702	0.1685	0.2007	0.1985	RANDOM	25.982

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]
1.9			0.02		-1.92

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.772
r_dihedral_angle_4_deg	21.62
r_dihedral_angle_3_deg	16.48
r_dihedral_angle_1_deg	4.979
r_scangle_it	4.069
r_scbond_it	2.433
r_angle_refined_deg	1.548
r_mcangle_it	1.29
r_mcbond_it	0.856
r_nbtor_refined	0.304
r_symmetry_hbond_refined	0.298
r_symmetry_vdw_refined	0.209
r_nbd_refined	0.203
r_xyhbond_nbd_refined	0.168
r_chiral_restr	0.113
r_bond_refined_d	0.016
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3011
Nucleic Acid Atoms
Solvent Atoms	155
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
SHELXD	phasing
MLPHARE	phasing
DM	phasing
SOLVE	phasing
RESOLVE	phasing
HKL-3000	phasing