3C7J

Crystal structure of transcriptional regulator (GntR family member) from Pseudomonas syringae pv. tomato str. DC3000

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	277	10% Propanol, 0.1M Imidazole pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.95	58.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.954	α = 90
b = 132.768	β = 90
c = 170.461	γ = 90

Symmetry
Space Group	C 2 2 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	Mirrors	2007-09-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.9794	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	2.1	45	98.1	0.08	30.1	6	37685	37612		2

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	2.1	2.14	96		0.649	2.5	5.8

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 (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.1	45	36788	1838	97.9	0.182	0.182	0.18	0.227	RANDOM	24.956

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]
1.08			-0.3		-0.78

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.302
r_dihedral_angle_4_deg	20.888
r_dihedral_angle_3_deg	13.192
r_dihedral_angle_1_deg	5.299
r_scangle_it	3.214
r_scbond_it	2.466
r_angle_refined_deg	1.481
r_mcangle_it	1.185
r_angle_other_deg	1.02
r_mcbond_it	0.99
r_symmetry_vdw_other	0.269
r_nbd_refined	0.222
r_nbd_other	0.192
r_symmetry_vdw_refined	0.189
r_mcbond_other	0.189
r_symmetry_hbond_refined	0.186
r_xyhbond_nbd_refined	0.174
r_nbtor_refined	0.172
r_nbtor_other	0.087
r_chiral_restr	0.085
r_bond_refined_d	0.018
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3662
Nucleic Acid Atoms
Solvent Atoms	354
Heterogen Atoms	2

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
SHELXD	phasing
Coot	model building
MLPHARE	phasing
PHENIX	phasing
REFMAC	phasing