4D7M

TetR(D) in complex with anhydrotetracycline and magnesium


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2TRTPDB ENTRY 2TRT

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1950 MM TRIS-HCL PH 9.0, 1 M (NH4)2SO4, 70 MM NACL, 10 MM MGCL2
Crystal Properties
Matthews coefficientSolvent content
2.0740.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.628α = 90
b = 65.628β = 90
c = 178.598γ = 90
Symmetry
Space GroupI 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX SX-165mmMIRRORS2004-05-01MSINGLE 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
11.5528.999.20.0626.510.828546-328.7
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)
11.551.6599.41.082.9410.4

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 2TRT1.5561.627199134799.240.178160.176270.21669RANDOM29.096
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]
0.470.47-0.93
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.589
r_dihedral_angle_4_deg16.638
r_dihedral_angle_3_deg13.342
r_dihedral_angle_1_deg5.39
r_mcangle_it2.864
r_scbond_it2.765
r_angle_refined_deg2.051
r_mcbond_it1.955
r_mcbond_other1.954
r_angle_other_deg0.907
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.589
r_dihedral_angle_4_deg16.638
r_dihedral_angle_3_deg13.342
r_dihedral_angle_1_deg5.39
r_mcangle_it2.864
r_scbond_it2.765
r_angle_refined_deg2.051
r_mcbond_it1.955
r_mcbond_other1.954
r_angle_other_deg0.907
r_chiral_restr0.258
r_bond_refined_d0.02
r_gen_planes_refined0.012
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_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 Atoms1641
Nucleic Acid Atoms
Solvent Atoms179
Heterogen Atoms41

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
AMoREphasing