6QJW

TetR(D) T103A mutant in complex with 7-chlortetracycline and magnesium


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2TCT 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP295Precipitant: 30%PEG 400, 0.1M MES pH 6.5, 60 mM MgCl2. Protein: 12.15 mg/mL protein in 100mM NaCl, 50 mM Tris buffer, pH 8.0, 4mM 7ClTc, 3M MgCl2. Protein/precipitant 1/1
Crystal Properties
Matthews coefficientSolvent content
2.2645.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.138α = 90
b = 68.138β = 90
c = 180.917γ = 90
Symmetry
Space GroupI 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 70mirror2014-10-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0071.5418

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
12.134.091000.136.856.851289625
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)
12.12.181000.4876.82

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2TCT2.134.0911569126699.470.226940.219880.29024RANDOM31.192
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]
0.480.48-0.95
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.92
r_dihedral_angle_4_deg17.085
r_dihedral_angle_3_deg16.337
r_dihedral_angle_1_deg7.59
r_long_range_B_refined5.424
r_long_range_B_other5.254
r_scangle_other3.146
r_mcangle_it2.601
r_mcangle_other2.6
r_scbond_it1.929
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.92
r_dihedral_angle_4_deg17.085
r_dihedral_angle_3_deg16.337
r_dihedral_angle_1_deg7.59
r_long_range_B_refined5.424
r_long_range_B_other5.254
r_scangle_other3.146
r_mcangle_it2.601
r_mcangle_other2.6
r_scbond_it1.929
r_scbond_other1.923
r_angle_refined_deg1.828
r_mcbond_it1.702
r_mcbond_other1.701
r_angle_other_deg1.432
r_chiral_restr0.084
r_bond_refined_d0.013
r_gen_planes_refined0.009
r_gen_planes_other0.002
r_bond_other_d0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1571
Nucleic Acid Atoms
Solvent Atoms109
Heterogen Atoms39

Software

Software
Software NamePurpose
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling
PHASERphasing