3DEU | pdb_00003deu

Crystal structure of transcription regulatory protein slyA from Salmonella typhimurium in complex with salicylate ligands

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2FBH	PDB entry 2FBH

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.2	298	20% PEG 300, 10% Glycerol, 0.1 M Phosphate/citrate buffer pH 4.2, 0.2 M Ammonium sulfate, 50 mM Sodium salicylate, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.73	54.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.382	α = 90
b = 78.019	β = 90
c = 84.385	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	MARMOSAIC 300 mm CCD	Adjustable focusing mirrors in K-B geometry	2007-11-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	1.37760	APS	23-ID-D

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	50	96.4	0.074	31.7	12.9	27988	27988			51.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2	2.07	90.8		1.1	7.1	2583

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 2FBH	2.3	20	18739	18739	928	97.79	0.229	0.229	0.228	0.2401	0.259	0.2629	RANDOM	64.71

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]
4.27			0.01		-4.28

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.865
r_dihedral_angle_4_deg	22.639
r_dihedral_angle_3_deg	20.7
r_dihedral_angle_1_deg	12.639
r_scangle_it	9.869
r_scbond_it	6.66
r_mcangle_it	4.354
r_mcbond_it	2.523
r_angle_refined_deg	1.986
r_angle_other_deg	1.01
r_mcbond_other	0.83
r_chiral_restr	0.116
r_bond_refined_d	0.011
r_gen_planes_refined	0.005
r_bond_other_d
r_gen_planes_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2110
Nucleic Acid Atoms
Solvent Atoms	19
Heterogen Atoms	60

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
MOLREP	phasing