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Crystal Structure of the Complex of Malachite Green Bound to QacR(E120Q), 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 3.34 63.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.157 α = 90 b = 104.157 β = 90 c = 97.982 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 ADSC QUANTUM 315 KOHZU: Double Crystal Si(111) 2005-08-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 1.0 ALS 8.2.2
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 2.4 35.7 100 0.085 6.1 7.2 23093 23093 1.7 48.87
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) 2.4 2.55 100 0.435 1.7 7.4 3362
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 2.42 35.69 21890 21722 1175 99.23 0.21601 0.21601 0.21361 0.2174 0.2609 0.2633 RANDOM 40.946
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] -0.4 -0.2 -0.4 0.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.082 r_dihedral_angle_4_deg 31.243 r_dihedral_angle_3_deg 15.122 r_dihedral_angle_1_deg 5.193 r_scangle_it 2.732 r_mcangle_it 2.148 r_scbond_it 1.952 r_mcbond_it 1.234 r_angle_refined_deg 1.056 r_angle_other_deg 0.827
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.082 r_dihedral_angle_4_deg 31.243 r_dihedral_angle_3_deg 15.122 r_dihedral_angle_1_deg 5.193 r_scangle_it 2.732 r_mcangle_it 2.148 r_scbond_it 1.952 r_mcbond_it 1.234 r_angle_refined_deg 1.056 r_angle_other_deg 0.827 r_symmetry_hbond_refined 0.335 r_symmetry_vdw_refined 0.212 r_nbd_refined 0.201 r_nbtor_refined 0.185 r_nbd_other 0.172 r_xyhbond_nbd_refined 0.157 r_mcbond_other 0.131 r_symmetry_vdw_other 0.127 r_nbtor_other 0.086 r_chiral_restr 0.062 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 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 3031 Nucleic Acid Atoms Solvent Atoms 83 Heterogen Atoms 95
Software Software Software Name Purpose REFMAC refinement BOS data collection MOSFLM data reduction SCALA data scaling MOLREP phasing