3BR3

Crystal Structure of the Complex of Ethidium Bound to QacR(E90Q), a Mutant of a Multidrug Binding Transcriptional Repressor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1JT6PDB entry 1JT6

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.62731:1 10mg/ml protein with 2.3M Ammonium sulfate with 100mM Sodium Acetate pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 273K
Crystal Properties
Matthews coefficientSolvent content
3.3663.43

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 104.148α = 90
b = 104.148β = 90
c = 98.564γ = 120
Symmetry
Space GroupP 62

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDNOIR-1Rosenbaum-Rock monochromator 1: high-resolution double-crystal sagittal focusing, Rosenbaum-Rock monochromator 2: double crystal, Rosenbaum-Rock vertical focusing mirror2007-06-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 4.2.21.0ALS4.2.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.846.041000.0617.37.5215047150471.9
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.82.91000.41.97.451517

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1JT62.841142761318770292.370.221820.221820.218440.29326RANDOM22.77
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]
0.220.110.22-0.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.655
r_dihedral_angle_3_deg13.129
r_dihedral_angle_4_deg10.273
r_dihedral_angle_1_deg4.384
r_scangle_it1.609
r_mcangle_it1.266
r_scbond_it1.005
r_angle_refined_deg0.8
r_angle_other_deg0.753
r_mcbond_it0.676
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.655
r_dihedral_angle_3_deg13.129
r_dihedral_angle_4_deg10.273
r_dihedral_angle_1_deg4.384
r_scangle_it1.609
r_mcangle_it1.266
r_scbond_it1.005
r_angle_refined_deg0.8
r_angle_other_deg0.753
r_mcbond_it0.676
r_nbd_refined0.204
r_nbtor_refined0.186
r_nbd_other0.15
r_symmetry_vdw_other0.135
r_xyhbond_nbd_refined0.13
r_symmetry_vdw_refined0.095
r_nbtor_other0.082
r_mcbond_other0.057
r_symmetry_hbond_refined0.046
r_chiral_restr0.045
r_bond_refined_d0.006
r_gen_planes_refined0.002
r_bond_other_d0.001
r_gen_planes_other0.001
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 AtomsNumber
Protein Atoms2961
Nucleic Acid Atoms
Solvent Atoms15
Heterogen Atoms64

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata collection
d*TREKdata reduction
d*TREKdata scaling
MOLREPphasing