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Crystal Structure of the Complex of Malachite Green 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 3.32 62.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.387 α = 90 b = 104.387 β = 90 c = 97.184 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) 2004-12-14 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 2.17 45.2 99.8 0.062 7.4 6.5 31839 31776 1.8 45.734
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) 2.17 2.23 100 0.42 1.8 5.3 4626
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 2.17 45.2 30246 29339 1560 97 0.22545 0.22545 0.22397 0.2242 0.25355 0.2519 RANDOM 38.991
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] 0.05 0.02 0.05 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.634 r_dihedral_angle_4_deg 25.55 r_dihedral_angle_3_deg 15.395 r_dihedral_angle_1_deg 4.827 r_scangle_it 2.977 r_mcangle_it 2.203 r_scbond_it 2.008 r_mcbond_it 1.231 r_angle_refined_deg 0.989 r_angle_other_deg 0.833
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.634 r_dihedral_angle_4_deg 25.55 r_dihedral_angle_3_deg 15.395 r_dihedral_angle_1_deg 4.827 r_scangle_it 2.977 r_mcangle_it 2.203 r_scbond_it 2.008 r_mcbond_it 1.231 r_angle_refined_deg 0.989 r_angle_other_deg 0.833 r_symmetry_vdw_refined 0.242 r_nbd_refined 0.188 r_nbtor_refined 0.185 r_nbd_other 0.166 r_xyhbond_nbd_refined 0.136 r_symmetry_hbond_refined 0.135 r_symmetry_vdw_other 0.129 r_mcbond_other 0.128 r_nbtor_other 0.085 r_chiral_restr 0.061 r_bond_refined_d 0.009 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 2947 Nucleic Acid Atoms Solvent Atoms 85 Heterogen Atoms 65
Software Software Software Name Purpose REFMAC refinement BOS data collection MOSFLM data reduction SCALA data scaling MOLREP phasing