6YR2

TetR(D) soaked with Tigecycline P4(1)2(1)2


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7291Native crystal soaked in 1M (NH4)2SO4, 0.2M NaCl, 0.05M Tris/HCl, pH 7.0, 0.142 mM TigeTC, 2mM MgCl2, 14hours.
Crystal Properties
Matthews coefficientSolvent content
2.2444.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.339α = 90
b = 68.339β = 90
c = 178.397γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 702009-11-11MSINGLE 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
11.9542.597.90.1437.17.333177929
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)
11.952.0292.40.6391.44.52

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-VALUE2xpv1.9537.5331150156998.0760.2120.21020.237434.691
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]
0.4350.435-0.87
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.966
r_dihedral_angle_4_deg16.416
r_dihedral_angle_3_deg15.895
r_dihedral_angle_1_deg6.549
r_lrange_it5.199
r_lrange_other5.181
r_scangle_it3.273
r_scangle_other3.217
r_mcangle_it2.715
r_mcangle_other2.715
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.966
r_dihedral_angle_4_deg16.416
r_dihedral_angle_3_deg15.895
r_dihedral_angle_1_deg6.549
r_lrange_it5.199
r_lrange_other5.181
r_scangle_it3.273
r_scangle_other3.217
r_mcangle_it2.715
r_mcangle_other2.715
r_scbond_it2.02
r_angle_refined_deg1.964
r_scbond_other1.95
r_mcbond_it1.637
r_mcbond_other1.637
r_angle_other_deg1.538
r_symmetry_nbd_refined0.259
r_nbd_refined0.23
r_nbd_other0.205
r_symmetry_nbd_other0.19
r_xyhbond_nbd_refined0.184
r_nbtor_refined0.175
r_ncsr_local_group_10.147
r_symmetry_xyhbond_nbd_refined0.137
r_chiral_restr0.091
r_symmetry_nbtor_other0.091
r_symmetry_xyhbond_nbd_other0.043
r_bond_refined_d0.014
r_gen_planes_refined0.01
r_bond_other_d0.003
r_gen_planes_other0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3196
Nucleic Acid Atoms
Solvent Atoms165
Heterogen Atoms61

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata reduction
CrystalCleardata scaling
PHASERphasing