5FKN

TetR(D) T103A mutant in complex with anhydrotetracycline and magnesium, P4(3)2(1)2


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4D7MPDB ENTRY 4D7M

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.52951.4 M (NH4)2SO4, 0.1 M MES PH 6.5, 110 MM NACL, 1 MM 5A,6-ANHYDROTETRACYCLINE, 7.5 MM MGCL2 AT 295 K
Crystal Properties
Matthews coefficientSolvent content
2.2344.76

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.95α = 90
b = 67.95β = 90
c = 179.45γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDMIRRORSMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.2BESSY14.2

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
11.863.698.80.0723.712.839516-332.5
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)
11.81.8598.20.812.610.8

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 REPLACEMENTTHROUGHOUTPDB ENTRY 4D7M1.863.5537514198598.840.225330.223760.25542RANDOM29.745
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]
1.171.17-2.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.193
r_dihedral_angle_4_deg14.874
r_dihedral_angle_3_deg13.359
r_dihedral_angle_1_deg4.996
r_mcangle_it1.811
r_scbond_it1.334
r_angle_refined_deg1.299
r_mcbond_it1.106
r_mcbond_other1.106
r_angle_other_deg0.761
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.193
r_dihedral_angle_4_deg14.874
r_dihedral_angle_3_deg13.359
r_dihedral_angle_1_deg4.996
r_mcangle_it1.811
r_scbond_it1.334
r_angle_refined_deg1.299
r_mcbond_it1.106
r_mcbond_other1.106
r_angle_other_deg0.761
r_chiral_restr0.075
r_bond_refined_d0.009
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3164
Nucleic Acid Atoms
Solvent Atoms238
Heterogen Atoms75

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing