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Crystal Structure of the Complex of Rhodamine 6G 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 3.8 67.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 171.726 α = 90 b = 171.746 β = 90 c = 94.785 γ = 90
Symmetry Space Group P 42 21 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 CCD NOIR-1 Rosenbaum-Rock monochromator 1: high-resolution double-crystal sagittal focusing, Rosenbaum-Rock monochromator 2: double crystal, Rosenbaum-Rock vertical focusing mirror 2007-08-08 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 49.03 100 0.061 18.1 7.52 31603 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) 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 2.9 49.03 30359 30004 1599 98.83 0.24395 0.24395 0.24183 0.2433 0.28449 0.2819 RANDOM 65.546
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] -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.548 r_dihedral_angle_3_deg 16.633 r_dihedral_angle_4_deg 8.451 r_dihedral_angle_1_deg 4.986 r_scangle_it 1.583 r_mcangle_it 1.465 r_scbond_it 0.972 r_angle_refined_deg 0.907 r_mcbond_it 0.784 r_angle_other_deg 0.775
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.548 r_dihedral_angle_3_deg 16.633 r_dihedral_angle_4_deg 8.451 r_dihedral_angle_1_deg 4.986 r_scangle_it 1.583 r_mcangle_it 1.465 r_scbond_it 0.972 r_angle_refined_deg 0.907 r_mcbond_it 0.784 r_angle_other_deg 0.775 r_nbd_refined 0.216 r_nbtor_refined 0.192 r_nbd_other 0.16 r_symmetry_vdw_other 0.149 r_symmetry_vdw_refined 0.147 r_xyhbond_nbd_refined 0.13 r_symmetry_hbond_refined 0.103 r_nbtor_other 0.084 r_mcbond_other 0.054 r_chiral_restr 0.049 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 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 5856 Nucleic Acid Atoms Solvent Atoms 9 Heterogen Atoms 196
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection d*TREK data reduction d*TREK data scaling MOLREP phasing