3B6A | pdb_00003b6a

Crystal structure of the Streptomyces coelicolor TetR family protein ActR in complex with actinorhodin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2OPTPDB entry 2OPT

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.529315% PEG4000, 100 mM sodium acetate, 40 mM Tris, 25 mM KCl, 0.5 mM DTT, 15 mg/mL protein, 0.3 uL of 17 mM actinorhodin, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.4349.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.88α = 89.56
b = 79β = 89.92
c = 107.19γ = 89.88
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4collimating and focusing mirrors2006-10-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X12C1.1NSLSX12C

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
13.0537.12960.05510.61.883455111
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
3.053.129970.2692.41.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 2OPT3.0537.122979793985.090.260770.259880.260.288350.28RANDOM59.765
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]
-3.880.18-0.087.50.21-3.63
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.21
r_dihedral_angle_3_deg23.368
r_dihedral_angle_4_deg21.832
r_dihedral_angle_1_deg7.129
r_angle_refined_deg1.552
r_scangle_it1.404
r_angle_other_deg1.24
r_scbond_it0.854
r_mcangle_it0.619
r_mcbond_it0.338
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms12788
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms400

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
d*TREKdata reduction
d*TREKdata scaling
CCP4phasing
Cootmodel building