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Crystal structure of the MarR family transcriptional regulator from Enterobacter soli strain LF7 bound to Indole 3 acetic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7KUA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M Bis-Tris: HCl, pH 6.5, 2 M Ammonium Sulfate
Crystal Properties Matthews coefficient Solvent content 2.42 49.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.699 α = 90 b = 117.699 β = 90 c = 74.14 γ = 120
Symmetry Space Group P 32 2 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 PIXEL DECTRIS PILATUS3 6M 2020-11-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.0332 APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.76 50 99.1 0.156 0.164 0.052 7.9 9.5 15270
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.76 2.81 90 1.234 1.364 0.561 0.653 4.5
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 7KUA 2.77 46.14 14495 765 98.83 0.2356 0.2333 0.2327 0.2762 0.273 RANDOM 72.519
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] 0.9 0.45 0.9 -2.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.055 r_dihedral_angle_4_deg 19.852 r_dihedral_angle_3_deg 19.279 r_dihedral_angle_1_deg 7.268 r_angle_refined_deg 1.925 r_angle_other_deg 1.509 r_chiral_restr 0.094 r_bond_refined_d 0.015 r_gen_planes_refined 0.009 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.055 r_dihedral_angle_4_deg 19.852 r_dihedral_angle_3_deg 19.279 r_dihedral_angle_1_deg 7.268 r_angle_refined_deg 1.925 r_angle_other_deg 1.509 r_chiral_restr 0.094 r_bond_refined_d 0.015 r_gen_planes_refined 0.009 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2754 Nucleic Acid Atoms Solvent Atoms 4 Heterogen Atoms 40
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction