3B6C | pdb_00003b6c

Crystal structure of the Streptomyces coelicolor TetR family protein ActR in complex with (S)-DNPA


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.529314% PEG4000, 91mM sodium acetate, 45mM Bis-Tris, 23mM KCl, 9.1mM taurine, 4.6mM Tris, 0.45mM DTT and, after dehydration, less than 100 ug (S)-DNPA, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2846.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.969α = 90
b = 79.396β = 90
c = 103.453γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4collimating and focusing mirrors2006-11-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X8C1.1NSLSX8C

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
12.349.2392.10.04717.64.631945811
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)
2.32.3895.70.2114.34.47

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb entry 2OPT2.341.85194581405474370.040.246050.243920.26070.287030.3115RANDOM83.439
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]
-55.96-0.96
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.099
r_dihedral_angle_4_deg23.685
r_dihedral_angle_3_deg21.245
r_angle_other_deg9.262
r_dihedral_angle_1_deg6.666
r_scangle_it2.81
r_mcangle_it2.404
r_scbond_it1.829
r_mcbond_it1.354
r_angle_refined_deg0.92
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.099
r_dihedral_angle_4_deg23.685
r_dihedral_angle_3_deg21.245
r_angle_other_deg9.262
r_dihedral_angle_1_deg6.666
r_scangle_it2.81
r_mcangle_it2.404
r_scbond_it1.829
r_mcbond_it1.354
r_angle_refined_deg0.92
r_symmetry_hbond_refined0.431
r_nbd_other0.419
r_symmetry_vdw_refined0.343
r_nbtor_refined0.335
r_nbd_refined0.3
r_xyhbond_nbd_refined0.269
r_nbtor_other0.245
r_chiral_restr0.078
r_gen_planes_refined0.012
r_bond_refined_d0.007
r_bond_other_d0.002
r_gen_planes_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 Atoms3082
Nucleic Acid Atoms
Solvent Atoms146
Heterogen Atoms66

Software

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