☰ Navigation Tabs
Flavonoid-responsive Regulator FrrA in complex with (R,S)-Naringenin
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
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 0.1881 0.2189 0.2218 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
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