3CCY | pdb_00003ccy

Crystal structure of a TetR-family transcriptional regulator from Bordetella parapertussis 12822

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	289	1.5M NH4Cl, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.89	57.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.92	α = 90
b = 56.989	β = 90
c = 168.271	γ = 90

Symmetry
Space Group	I 2 2 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	ADSC QUANTUM 315	Mirrors	2007-12-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97904	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	29	99.6	0.114	22.4	6.2	18617	18617

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	2.06	97.6		0.672	2.17	5.5	1505

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	2.01	28.98	17644	17644	957	99.13	0.20036	0.20036	0.19826	0.1967	0.24183	0.2408	RANDOM	40.686

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]
-0.03			0.33		-0.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.311
r_dihedral_angle_4_deg	17.879
r_dihedral_angle_3_deg	17.743
r_dihedral_angle_1_deg	5.157
r_scangle_it	3.543
r_scbond_it	2.513
r_mcangle_it	1.524
r_angle_refined_deg	1.437
r_mcbond_it	1.082
r_nbtor_refined	0.302
r_symmetry_vdw_refined	0.27
r_nbd_refined	0.232
r_xyhbond_nbd_refined	0.148
r_symmetry_hbond_refined	0.127
r_chiral_restr	0.098
r_bond_refined_d	0.016
r_gen_planes_refined	0.006
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	1553
Nucleic Acid Atoms
Solvent Atoms	115
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
SHELXD	phasing
MLPHARE	phasing
DM	phasing
RESOLVE	phasing
HKL-3000	phasing