3F8F

Crystal structure of multidrug binding transcriptional regulator LmrR complexed with Daunomycin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3F8B 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP729825% PEG1500, 0.1M malonic acid/imidazol/boric (MIB) buffer, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.3447.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 35.45α = 90
b = 53.025β = 90
c = 147.116γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315mirrors2006-11-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.92ESRFID29

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.249.88499.40.0716.63.414655146552
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.3299.90.2730.2732.73.52074

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3F8B2.249.8814615138537621000.234650.232050.2796RANDOM24.347
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]
-1.783.32-1.54
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.087
r_dihedral_angle_3_deg18.916
r_dihedral_angle_4_deg13.174
r_dihedral_angle_1_deg5.729
r_scangle_it2.798
r_scbond_it1.687
r_mcangle_it1.131
r_mcbond_it0.684
r_angle_refined_deg0.651
r_nbtor_refined0.316
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.087
r_dihedral_angle_3_deg18.916
r_dihedral_angle_4_deg13.174
r_dihedral_angle_1_deg5.729
r_scangle_it2.798
r_scbond_it1.687
r_mcangle_it1.131
r_mcbond_it0.684
r_angle_refined_deg0.651
r_nbtor_refined0.316
r_nbd_refined0.217
r_symmetry_vdw_refined0.183
r_xyhbond_nbd_refined0.167
r_symmetry_hbond_refined0.166
r_chiral_restr0.063
r_bond_refined_d0.016
r_gen_planes_refined0.001
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1832
Nucleic Acid Atoms
Solvent Atoms43
Heterogen Atoms38

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection