6RBL

TETR(D) E147A MUTANT IN COMPLEX WITH DOXYCYCLINE AND MAGNESIUM


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6FPL 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP295Precipitant: 2.0M (NH4)2SO4, 3% PEG 400, 0.1M MES pH 6.5, Protein: 0.1mL protein, 0.1,L 2mM doxyTc, 0.001mL 3M MgCl2, 100mM NaCl, 50mM Tris pH8.0, 1/3 protein/precipitant
Crystal Properties
Matthews coefficientSolvent content
2.2545.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.3α = 90
b = 68.3β = 90
c = 179.4γ = 90
Symmetry
Space GroupI 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 70mirror2007-04-18MSINGLE 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
11.934.1799.40.09912.37.11712621
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)
11.91.9798.20.3711.94.29

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 REPLACEMENTTHROUGHOUT6FPL1.934.1715434130697.130.212420.209410.2464RANDOM21.97
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]
0.280.28-0.56
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.909
r_dihedral_angle_4_deg16.371
r_dihedral_angle_3_deg13.706
r_dihedral_angle_1_deg6.069
r_long_range_B_refined3.441
r_long_range_B_other3.354
r_scangle_other1.971
r_mcangle_it1.818
r_mcangle_other1.817
r_angle_refined_deg1.772
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.909
r_dihedral_angle_4_deg16.371
r_dihedral_angle_3_deg13.706
r_dihedral_angle_1_deg6.069
r_long_range_B_refined3.441
r_long_range_B_other3.354
r_scangle_other1.971
r_mcangle_it1.818
r_mcangle_other1.817
r_angle_refined_deg1.772
r_angle_other_deg1.463
r_scbond_other1.235
r_scbond_it1.23
r_mcbond_it1.084
r_mcbond_other1.084
r_chiral_restr0.083
r_bond_refined_d0.012
r_gen_planes_refined0.01
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 Atoms1601
Nucleic Acid Atoms
Solvent Atoms161
Heterogen Atoms39

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata reduction
CrystalCleardata scaling
PHASERphasing