2X9D

Tet repressor (class D) in complex with iso-7-chlortetracycline


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP80.002ML PROTEIN/COMPLEX (0.050 ML TETR(D) (C = 17.3 MG/ML)50 ML 2MM ISO-CLTC) PLUS ML BUFFER (50 MM TRIS PH 8, 1.1 M (NH4)2SO4, 100 MM NACL, 10 MM MGCL2) HANGING DROP AGAINST 0.5 ML BUFFER
Crystal Properties
Matthews coefficientSolvent content
2.2745.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.253α = 90
b = 68.253β = 90
c = 179.271γ = 90
Symmetry
Space GroupI 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH SX-165MIRRORS2004-03-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X13EMBL/DESY, HAMBURGX13

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
12.3463.7980.079.74.48912145.2
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)
12.342.39760.641.783.44

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2TCT2.3463.76820991297.640.238260.233660.27974RANDOM48.08
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]
1.521.52-3.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.182
r_dihedral_angle_4_deg16.913
r_dihedral_angle_3_deg15.233
r_dihedral_angle_1_deg5.972
r_scangle_it2.409
r_scbond_it1.591
r_angle_refined_deg1.447
r_mcangle_it1.119
r_angle_other_deg0.944
r_mcbond_it0.618
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.182
r_dihedral_angle_4_deg16.913
r_dihedral_angle_3_deg15.233
r_dihedral_angle_1_deg5.972
r_scangle_it2.409
r_scbond_it1.591
r_angle_refined_deg1.447
r_mcangle_it1.119
r_angle_other_deg0.944
r_mcbond_it0.618
r_mcbond_other0.119
r_chiral_restr0.078
r_bond_refined_d0.012
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_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 Atoms1544
Nucleic Acid Atoms
Solvent Atoms64
Heterogen Atoms37

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
REFMACphasing