6G8H

Flavonoid-responsive Regulator FrrA in complex with (R,S)-Naringenin

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6G87

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		291	6mg/ml FrrA in 20 mM Na2HPO4, 50 mM imidazole, pH 7.5, 50 mM NaCl with equimolar naringenin in 70% Ethanol. Precipitant 16,5 % PEG 8000; 0.1 M CHES, pH 9.5.

Crystal Properties
Matthews coefficient	Solvent content
2.88	57.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 118.709	α = 90
b = 118.709	β = 90
c = 78.354	γ = 90

Symmetry
Space Group	P 43

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS3 S 6M		2015-10-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	0.97630	PETRA III, EMBL c/o DESY	P13 (MX1)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	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	2.312	118.71	95.2	0.094	0.998	9.74	3.35		67523			81.2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.312	2.54	72.2		1.76	0.2	0.54	2.76

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6G87	2.6	118.709	33724	1624	99.947	0.184	0.1825	0.19	0.2189	0.22	75.586

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]
-1.391			-1.391		2.783

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.54
r_dihedral_angle_4_deg	21.305
r_dihedral_angle_3_deg	18.979
r_lrange_it	10.843
r_lrange_other	10.843
r_scangle_it	9.268
r_scangle_other	9.267
r_dihedral_angle_1_deg	6.456
r_mcangle_it	6.456
r_mcangle_other	6.455
r_scbond_it	5.937
r_scbond_other	5.936
r_mcbond_it	4.413
r_mcbond_other	4.408
r_angle_refined_deg	1.793
r_angle_other_deg	1.321
r_symmetry_xyhbond_nbd_refined	0.382
r_nbd_other	0.226
r_nbd_refined	0.212
r_symmetry_nbd_refined	0.205
r_xyhbond_nbd_refined	0.2
r_symmetry_nbd_other	0.18
r_nbtor_refined	0.172
r_ncsr_local_group_6	0.124
r_ncsr_local_group_4	0.122
r_ncsr_local_group_3	0.117
r_ncsr_local_group_1	0.115
r_symmetry_nbtor_other	0.09
r_chiral_restr	0.089
r_symmetry_xyhbond_nbd_other	0.088
r_ncsr_local_group_2	0.087
r_ncsr_local_group_5	0.086
r_chiral_restr_other	0.04
r_bond_refined_d	0.011
r_gen_planes_refined	0.008
r_xyhbond_nbd_other	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	6068
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	131

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing