2Q24 | pdb_00002q24

Crystal structure of TetR transcriptional regulator SCO0520 from Streptomyces coelicolor

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4	273	0.1M Na(OAc) pH 4.0, 0.2M Ammonium acetate, 26% PEG 3350, 4% Sucrose, 2.5mM Tylosin tartrate, VAPOR DIFFUSION, HANGING DROP, temperature 273K

Crystal Properties
Matthews coefficient	Solvent content
2.17	43.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.295	α = 90
b = 146.152	β = 90
c = 47.305	γ = 90

Symmetry
Space Group	P 21 21 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	APS-1	MIRROR	2006-10-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM	0.97907	APS	19-BM

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.8	50	99.6	0.076	0.076	33.658	5.5	34267	34267		-3	26.05

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.82	95.4		0.416	0.416	3.2	5.2

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-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.8	50	34207	34207	1730	100	0.193	0.193	0.191	0.19	0.225	0.23	RANDOM	29.78

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]
0.1			0.42		-0.52

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.315
r_dihedral_angle_4_deg	18.178
r_dihedral_angle_3_deg	14.052
r_dihedral_angle_1_deg	11.652
r_scangle_it	4.754
r_scbond_it	3.118
r_mcangle_it	1.575
r_mcbond_it	1.568
r_angle_refined_deg	1.559
r_nbtor_refined	0.307
r_symmetry_vdw_refined	0.269
r_nbd_refined	0.215
r_symmetry_hbond_refined	0.152
r_xyhbond_nbd_refined	0.15
r_chiral_restr	0.123
r_bond_refined_d	0.018
r_gen_planes_refined	0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2558
Nucleic Acid Atoms
Solvent Atoms	273
Heterogen Atoms	5

Software

Software
Software Name	Purpose
HKL-3000	data collection
HKL-2000	data reduction
HKL-3000	phasing
MLPHARE	phasing
DM	model building
SHELXD	phasing
RESOLVE	model building
ARP/wARP	model building
Coot	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing
SHELXE	model building
RESOLVE	phasing
CCP4	phasing