3SZT | pdb_00003szt

Quorum Sensing Control Repressor, QscR, Bound to N-3-oxo-dodecanoyl-L-Homoserine Lactone

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		SCRWL MODEL OF AHL AND DNA-BINDING DOMAINS OF TRAR

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.83	277	0.168 M magnesium acetate, 21.8% PEG8000, 0.1 M Tris, pH 7.83, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.5	50.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 94.862	α = 90
b = 94.862	β = 90
c = 104.953	γ = 120

Symmetry
Space Group	P 31 2 1

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	NOIR-1		2009-07-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 4.2.2	1.0000	ALS	4.2.2

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	2.5	25	100	0.052	0.052	40	11.9	19230	19230			61.9

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	2.5	2.59	99.6		0.41	4.8	12.2	1882

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	SCRWL MODEL OF AHL AND DNA-BINDING DOMAINS OF TRAR	2.55	15	17116	17116	953	99.58	0.2249	0.2249	0.22264	0.23	0.26594	0.27	RANDOM	78.553

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]
-0.39	-0.19		-0.39		0.58

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	26.967
r_dihedral_angle_4_deg	15.115
r_dihedral_angle_3_deg	13.946
r_dihedral_angle_1_deg	4.14
r_mcangle_it	2.416
r_scangle_it	1.621
r_mcbond_it	1.573
r_angle_refined_deg	1.295
r_scbond_it	1.117
r_chiral_restr	0.088
r_bond_refined_d	0.01
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3608
Nucleic Acid Atoms
Solvent Atoms	20
Heterogen Atoms	43

Software

Software
Software Name	Purpose
Blu-Ice	data collection
JBluIce-EPICS	data collection
PHASER	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling