6G8G | pdb_00006g8g

Flavonoid-responsive Regulator FrrA in complex with Genistein

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, 100 mM imidazole, pH 7.5, 50 mM NaCl with equimolar Genistein in 70% Ethanol. Precipitant 20 % PEG 8000; 0.1 M CHES, pH 9.5.

Crystal Properties
Matthews coefficient	Solvent content
2.89	57.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 119.044	α = 90
b = 119.044	β = 90
c = 78.305	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 PILATUS 6M-F		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	2.599	119.1	99.1	0.091	0.998	11.52	3.44		65566			76.3

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	2.599	2.7	97.7		1.52	0.279	0.82	3.35

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	6G87	2.6	119.04	32099	1719	99.75	0.18984	0.18839	0.2	0.21644	0.22	RANDOM	75.677

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]
-0.72			-0.72		1.43

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.54
r_dihedral_angle_4_deg	19.535
r_dihedral_angle_3_deg	18.295
r_long_range_B_other	11.38
r_long_range_B_refined	11.379
r_scangle_other	9.58
r_scbond_it	6.128
r_scbond_other	6.127
r_mcangle_it	6.023
r_mcangle_other	6.022
r_dihedral_angle_1_deg	5.477
r_mcbond_it	4.107
r_mcbond_other	4.104
r_angle_refined_deg	1.678
r_angle_other_deg	1.438
r_chiral_restr	0.084
r_bond_refined_d	0.013
r_gen_planes_refined	0.009
r_bond_other_d	0.007
r_gen_planes_other	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	6115
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	131

Software

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