6FPM

TetR(D) T103A mutant in complex with tetracycline and magnesium


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6FPL 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52950.1M MES pH 6.5, 24% PEG 400, 70mM MgCl2. 2mM TC, 14.55mg/ml protein
Crystal Properties
Matthews coefficientSolvent content
2.2946.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.71α = 90
b = 68.71β = 90
c = 180.47γ = 90
Symmetry
Space GroupI 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2011-12-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.20.95BESSY14.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
11.8564.2299.60.0610.05924.8914.11902642.9
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)
11.851.8997.21.471.913.44

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 REPLACEMENTTHROUGHOUT6FPL1.8564.211804797999.610.221460.219090.26727RANDOM45.825
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]
0.650.65-1.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.15
r_dihedral_angle_4_deg19.384
r_dihedral_angle_3_deg15.508
r_long_range_B_other6.815
r_long_range_B_refined6.814
r_dihedral_angle_1_deg5.955
r_scangle_other4.443
r_mcangle_it4.237
r_mcangle_other4.235
r_scbond_it2.88
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.15
r_dihedral_angle_4_deg19.384
r_dihedral_angle_3_deg15.508
r_long_range_B_other6.815
r_long_range_B_refined6.814
r_dihedral_angle_1_deg5.955
r_scangle_other4.443
r_mcangle_it4.237
r_mcangle_other4.235
r_scbond_it2.88
r_scbond_other2.878
r_mcbond_it2.825
r_mcbond_other2.824
r_angle_refined_deg1.877
r_angle_other_deg0.878
r_chiral_restr0.107
r_bond_refined_d0.018
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 Atoms1552
Nucleic Acid Atoms
Solvent Atoms68
Heterogen Atoms37

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing