6RGX

TETR(D) N82A MUTANT IN COMPLEX WITH DOXYCYCLINE AND MAGNESIUM


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5FKK 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP295precipitant: 0.1 M HEPES pH 7.5, 1.75M (NH4)2SO4, 5% PEG 400, 0.2M NaCl, protein: 0.1mL protein, 0.3mL 2mM doxyTc, 0.001mL 3M MgCl2, 100mM NaCl, 50mM Tris, pH 8.0, Protein/precipitant 2/2
Crystal Properties
Matthews coefficientSolvent content
2.2645.65

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.378α = 90
b = 68.378β = 90
c = 180.008γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 702011-08-05MSINGLE 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)Rrim I (All)Rpim 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
11.832.9499.80.1420.1490.04310.610.84048724.7
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.998.90.9351.0520.4672.14.7

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 REPLACEMENTTHROUGHOUT5FKK1.831.9838282203999.430.210750.209050.24309RANDOM27.671
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]
0.30.3-0.61
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.633
r_dihedral_angle_4_deg20.953
r_dihedral_angle_3_deg13.956
r_dihedral_angle_1_deg6.038
r_long_range_B_refined5.527
r_long_range_B_other5.506
r_scangle_other3.288
r_mcangle_it3.005
r_mcangle_other3.004
r_scbond_other2.017
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.633
r_dihedral_angle_4_deg20.953
r_dihedral_angle_3_deg13.956
r_dihedral_angle_1_deg6.038
r_long_range_B_refined5.527
r_long_range_B_other5.506
r_scangle_other3.288
r_mcangle_it3.005
r_mcangle_other3.004
r_scbond_other2.017
r_scbond_it2.013
r_mcbond_it1.798
r_mcbond_other1.798
r_angle_refined_deg1.797
r_angle_other_deg1.507
r_chiral_restr0.084
r_bond_refined_d0.013
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 Atoms3192
Nucleic Acid Atoms
Solvent Atoms262
Heterogen Atoms66

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata reduction
SCALAdata scaling
REFMACphasing