X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2TRT2TRT, 2TCT
experimental modelPDB 2TCT2TRT, 2TCT

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5295Precipitant: 2M (NH4)2SO4, 6% PEG400, 0.1M Tris pH8.5. 19.65mg/ml Protein, 2mM Tetracycline, 3M MgCl2.
Crystal Properties
Matthews coefficientSolvent content
2.2946.32

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.779α = 90
b = 68.779β = 90
c = 180.14γ = 90
Symmetry
Space GroupI 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 922007-05-07MSINGLE 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
1234.3998.70.06216.19.551492048.8
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)
122.0791.30.5252.36.73

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 REPLACEMENTTHROUGHOUT2TRT, 2TCT234.3913663101697.10.225790.222130.27236RANDOM48.063
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]
-0.16-0.160.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.701
r_dihedral_angle_4_deg19.59
r_dihedral_angle_3_deg17.011
r_long_range_B_refined8.273
r_long_range_B_other8.247
r_dihedral_angle_1_deg5.973
r_scangle_other4.994
r_mcangle_it4.876
r_mcangle_other4.874
r_mcbond_it3.175
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.701
r_dihedral_angle_4_deg19.59
r_dihedral_angle_3_deg17.011
r_long_range_B_refined8.273
r_long_range_B_other8.247
r_dihedral_angle_1_deg5.973
r_scangle_other4.994
r_mcangle_it4.876
r_mcangle_other4.874
r_mcbond_it3.175
r_mcbond_other3.175
r_scbond_it3.102
r_scbond_other3.102
r_angle_refined_deg1.738
r_angle_other_deg0.835
r_chiral_restr0.089
r_bond_refined_d0.017
r_gen_planes_refined0.008
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1561
Nucleic Acid Atoms
Solvent Atoms99
Heterogen Atoms15

Software

Software
Software NamePurpose
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling
PHASERphasing