4XK4

E. coli transcriptional regulator RUTR with dihydrouracil

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4JYK

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	289	200 nl of 10 mg/ml protein in 10 mM HEPES pH 7.5, 500 mM NaCl, 5 mM dihydrouracil was mixed with 200 nl 50 mM Ammonium Slufate, 50 mM BIS-TRIS, pH 6.5, 30% (v/v) Pentaerythirtol ethoxylate and suspended over a reservoir of 1.5M NaCl

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.892	α = 88.37
b = 55.672	β = 88.8
c = 85.242	γ = 62.37

Symmetry
Space Group	P 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	MARMOSAIC 300 mm CCD	Beryllium Lenses	2014-11-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97856	APS	21-ID-G

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	2.27	50.01	97.5	0.056	14.6	2.2	81777	37742

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	2.27	2.31	91		0.55	1.67	2.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4JYK	2.27	50.01	35540	1827	97.51	0.19566	0.19407	0.22539	RANDOM	52.064

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]
2.31	-2.29	-1.92	-1.39	0.74	-2.56

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.706
r_dihedral_angle_3_deg	15.122
r_dihedral_angle_4_deg	14.276
r_dihedral_angle_1_deg	4.989
r_long_range_B_refined	4.03
r_long_range_B_other	3.975
r_scangle_other	2.578
r_mcangle_it	2.093
r_mcangle_other	2.093
r_scbond_it	1.558
r_scbond_other	1.558
r_angle_refined_deg	1.354
r_angle_other_deg	1.351
r_mcbond_it	1.326
r_mcbond_other	1.326
r_chiral_restr	0.078
r_gen_planes_refined	0.014
r_gen_planes_other	0.012
r_bond_refined_d	0.01
r_bond_other_d	0.007
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6133
Nucleic Acid Atoms
Solvent Atoms	238
Heterogen Atoms	32

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
PDB_EXTRACT	data extraction
HKL-3000	data scaling
HKL-3000	phasing