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Crystal structure of the MarR family transcriptional regulator from Acineotobacter baumannii 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 CHES: NaOH, pH 9.5, 30 % (w/v) PEG 3000
Crystal Properties Matthews coefficient Solvent content 2.37 48.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.672 α = 90 b = 72.672 β = 90 c = 125.125 γ = 120
Symmetry Space Group P 61 2 2
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 2020-11-14 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 2.35 50 96.8 0.101 0.105 0.026 7.1 14.4 8439
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 2.35 2.39 77.5 0.734 0.81 0.333 0.782 5.1
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 2.35 36.36 7995 404 96.82 0.216 0.214 0.2199 0.2586 0.2621 RANDOM 63.626
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] -1.04 -0.52 -1.04 3.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.976 r_dihedral_angle_4_deg 23.505 r_dihedral_angle_3_deg 18.582 r_dihedral_angle_1_deg 7.224 r_angle_refined_deg 1.787 r_angle_other_deg 1.533 r_chiral_restr 0.086 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.976 r_dihedral_angle_4_deg 23.505 r_dihedral_angle_3_deg 18.582 r_dihedral_angle_1_deg 7.224 r_angle_refined_deg 1.787 r_angle_other_deg 1.533 r_chiral_restr 0.086 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1329 Nucleic Acid Atoms Solvent Atoms 9 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling PHASER phasing PDB_EXTRACT data extraction