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Crystal Structure of the Complex of Ethidium Bound to QacR(E90Q), a Mutant of a Multidrug Binding Transcriptional Repressor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JT6 PDB entry 1JT6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 273 1:1 10mg/ml protein with 2.3M Ammonium sulfate with 100mM Sodium Acetate pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 273K
Crystal Properties Matthews coefficient Solvent content 3.36 63.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.148 α = 90 b = 104.148 β = 90 c = 98.564 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD NOIR-1 Rosenbaum-Rock monochromator 1: high-resolution double-crystal sagittal focusing, Rosenbaum-Rock monochromator 2: double crystal, Rosenbaum-Rock vertical focusing mirror 2007-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 4.2.2 1.0 ALS 4.2.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 2.8 46.04 100 0.061 7.3 7.52 15047 15047 1.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.9 100 0.4 1.9 7.45 1517
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB entry 1JT6 2.8 41 14276 13187 702 92.37 0.22182 0.22182 0.21844 0.2208 0.29326 0.293 RANDOM 22.77
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] 0.22 0.11 0.22 -0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.655 r_dihedral_angle_3_deg 13.129 r_dihedral_angle_4_deg 10.273 r_dihedral_angle_1_deg 4.384 r_scangle_it 1.609 r_mcangle_it 1.266 r_scbond_it 1.005 r_angle_refined_deg 0.8 r_angle_other_deg 0.753 r_mcbond_it 0.676
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.655 r_dihedral_angle_3_deg 13.129 r_dihedral_angle_4_deg 10.273 r_dihedral_angle_1_deg 4.384 r_scangle_it 1.609 r_mcangle_it 1.266 r_scbond_it 1.005 r_angle_refined_deg 0.8 r_angle_other_deg 0.753 r_mcbond_it 0.676 r_nbd_refined 0.204 r_nbtor_refined 0.186 r_nbd_other 0.15 r_symmetry_vdw_other 0.135 r_xyhbond_nbd_refined 0.13 r_symmetry_vdw_refined 0.095 r_nbtor_other 0.082 r_mcbond_other 0.057 r_symmetry_hbond_refined 0.046 r_chiral_restr 0.045 r_bond_refined_d 0.006 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2961 Nucleic Acid Atoms Solvent Atoms 15 Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection d*TREK data reduction d*TREK data scaling MOLREP phasing