6G8H

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6G87 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2916mg/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 coefficientSolvent content
2.8857.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 118.709α = 90
b = 118.709β = 90
c = 78.354γ = 90
Symmetry
Space GroupP 43

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2015-10-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)0.97630PETRA III, EMBL c/o DESYP13 (MX1)

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim I (All)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.312118.7195.20.0940.9989.743.356752381.2
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.3122.5472.21.760.20.542.76

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE6G872.6118.70933724162499.9470.1840.18250.218975.586
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]
-1.391-1.3912.783
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.54
r_dihedral_angle_4_deg21.305
r_dihedral_angle_3_deg18.979
r_lrange_it10.843
r_lrange_other10.843
r_scangle_it9.268
r_scangle_other9.267
r_dihedral_angle_1_deg6.456
r_mcangle_it6.456
r_mcangle_other6.455
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.54
r_dihedral_angle_4_deg21.305
r_dihedral_angle_3_deg18.979
r_lrange_it10.843
r_lrange_other10.843
r_scangle_it9.268
r_scangle_other9.267
r_dihedral_angle_1_deg6.456
r_mcangle_it6.456
r_mcangle_other6.455
r_scbond_it5.937
r_scbond_other5.936
r_mcbond_it4.413
r_mcbond_other4.408
r_angle_refined_deg1.793
r_angle_other_deg1.321
r_symmetry_xyhbond_nbd_refined0.382
r_nbd_other0.226
r_nbd_refined0.212
r_symmetry_nbd_refined0.205
r_xyhbond_nbd_refined0.2
r_symmetry_nbd_other0.18
r_nbtor_refined0.172
r_ncsr_local_group_60.124
r_ncsr_local_group_40.122
r_ncsr_local_group_30.117
r_ncsr_local_group_10.115
r_symmetry_nbtor_other0.09
r_chiral_restr0.089
r_symmetry_xyhbond_nbd_other0.088
r_ncsr_local_group_20.087
r_ncsr_local_group_50.086
r_chiral_restr_other0.04
r_bond_refined_d0.011
r_gen_planes_refined0.008
r_xyhbond_nbd_other0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6068
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms131

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing