6YR1

TetR(D) soaked with Tigecycline I4(1)22


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5291Native crystal soaked in 1M (NH4)2SO4, 0.2M NaCl, 0.05M Tris/HCl, pH 7.0, 0.0142 mM Tigecycline, 2mM MgCl2, 22days
Crystal Properties
Matthews coefficientSolvent content
2.2745.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.459α = 90
b = 68.459β = 90
c = 180.44γ = 90
Symmetry
Space GroupI 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 70mirror2009-10-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0071.5418

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
12.331960.081115.83956559
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)
12.32.3888.60.4981.83.56

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-VALUE2xpv2.330.2956070495.8490.2370.23330.279266.175
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]
1.3011.301-2.601
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.646
r_dihedral_angle_3_deg19.517
r_dihedral_angle_4_deg15.741
r_lrange_it9.047
r_scangle_it6.959
r_dihedral_angle_1_deg6.787
r_mcangle_it6.099
r_scbond_it5.008
r_mcbond_it4.285
r_angle_refined_deg1.765
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.646
r_dihedral_angle_3_deg19.517
r_dihedral_angle_4_deg15.741
r_lrange_it9.047
r_scangle_it6.959
r_dihedral_angle_1_deg6.787
r_mcangle_it6.099
r_scbond_it5.008
r_mcbond_it4.285
r_angle_refined_deg1.765
r_nbtor_refined0.319
r_nbd_refined0.253
r_symmetry_nbd_refined0.24
r_symmetry_xyhbond_nbd_refined0.174
r_xyhbond_nbd_refined0.136
r_chiral_restr0.129
r_metal_ion_refined0.119
r_bond_refined_d0.008
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1555
Nucleic Acid Atoms
Solvent Atoms25
Heterogen Atoms46

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata reduction
CrystalCleardata scaling
PHASERphasing