7QZ7

Transcriptional regulator LmrR with bound daunomycin and with Trp-67 and Trp-96 replaced by 5,6,7-trifluoroTrp


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.1293Protein solution: 6 mg/ml in 20 mM Tris-HCl, pH 8.0, 300 mM NaCl. Reservoir solution: 100 mM SPG buffer, pH 6.1, 25% PEG 1500
Crystal Properties
Matthews coefficientSolvent content
2.1843.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102.495α = 90
b = 35.091β = 98.01
c = 68.074γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2015-09-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.91165ESRFID23-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
12.333.7198.60.0480.0590.0340.9989.12.91077259.39
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.3898.90.8651.0560.5990.5093

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3F8B2.333.7121075253998.150.22850.22450.290494.4184
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]
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1693
Nucleic Acid Atoms
Solvent Atoms2
Heterogen Atoms67

Software

Software
Software NamePurpose
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
PHENIXrefinement