4ABZ

TetR(D) in Complex with Tigecycline and Magnesium, co-crystallized


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8291Protein: 10.0 mg/mL TetR(D), 0.2M NaCl, 50 mM Tris/HCl, pH 8.0, 2mM [TigeTC], 2mM MgCl2. Precipitant: 1M (NH4)2SO4, 0.2M NaCl, 0.05M Tris/HCl, pH 8.0, 10mM MgCl2. Protein/precipitant 2+2 microL, against 0.5mL Precipitant.
Crystal Properties
Matthews coefficientSolvent content
2.7747

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.49α = 90
b = 68.49β = 90
c = 179.25γ = 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 14.20.950000BESSY14.2

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
11.855098.20.050.0533.9514.151842841
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.851.997.21.92.0414.19

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2xpv1.88648.4771736788098.2190.2150.21310.258337.603
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]
1.3351.335-2.67
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.08
r_dihedral_angle_4_deg22.541
r_dihedral_angle_3_deg16.243
r_dihedral_angle_1_deg6.634
r_lrange_it5.631
r_lrange_other5.631
r_scangle_it4.03
r_scangle_other4.03
r_mcangle_it3.27
r_mcangle_other3.269
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.08
r_dihedral_angle_4_deg22.541
r_dihedral_angle_3_deg16.243
r_dihedral_angle_1_deg6.634
r_lrange_it5.631
r_lrange_other5.631
r_scangle_it4.03
r_scangle_other4.03
r_mcangle_it3.27
r_mcangle_other3.269
r_scbond_it2.587
r_scbond_other2.585
r_mcbond_it2.22
r_mcbond_other2.217
r_angle_refined_deg1.982
r_angle_other_deg1.539
r_nbd_other0.242
r_nbd_refined0.237
r_symmetry_xyhbond_nbd_refined0.228
r_symmetry_nbd_other0.2
r_symmetry_nbd_refined0.193
r_nbtor_refined0.177
r_xyhbond_nbd_refined0.129
r_symmetry_nbtor_other0.093
r_chiral_restr0.089
r_xyhbond_nbd_other0.07
r_bond_refined_d0.014
r_metal_ion_refined0.011
r_gen_planes_refined0.01
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1550
Nucleic Acid Atoms
Solvent Atoms42
Heterogen Atoms46

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing