3BQZ

Crystal Structure of the Complex of Malachite Green 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
3.3262.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 104.387α = 90
b = 104.387β = 90
c = 97.184γ = 120
Symmetry
Space GroupP 62

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315KOHZU: Double Crystal Si(111)2004-12-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.21.0ALS8.2.2

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
12.1745.299.80.0627.46.531839317761.845.734
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)
2.172.231000.421.85.34626

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 1JT62.1745.230246293391560970.225450.225450.223970.25355RANDOM38.991
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]
0.050.020.05-0.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.634
r_dihedral_angle_4_deg25.55
r_dihedral_angle_3_deg15.395
r_dihedral_angle_1_deg4.827
r_scangle_it2.977
r_mcangle_it2.203
r_scbond_it2.008
r_mcbond_it1.231
r_angle_refined_deg0.989
r_angle_other_deg0.833
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.634
r_dihedral_angle_4_deg25.55
r_dihedral_angle_3_deg15.395
r_dihedral_angle_1_deg4.827
r_scangle_it2.977
r_mcangle_it2.203
r_scbond_it2.008
r_mcbond_it1.231
r_angle_refined_deg0.989
r_angle_other_deg0.833
r_symmetry_vdw_refined0.242
r_nbd_refined0.188
r_nbtor_refined0.185
r_nbd_other0.166
r_xyhbond_nbd_refined0.136
r_symmetry_hbond_refined0.135
r_symmetry_vdw_other0.129
r_mcbond_other0.128
r_nbtor_other0.085
r_chiral_restr0.061
r_bond_refined_d0.009
r_gen_planes_refined0.004
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 Atoms2947
Nucleic Acid Atoms
Solvent Atoms85
Heterogen Atoms65

Software

Software
Software NamePurpose
REFMACrefinement
BOSdata collection
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing