6RCR

TETR(D) H100A MUTANT IN COMPLEX WITH DOXYCYCLINE AND MAGNESIUM


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP295precipitant: 0.5M (NH4)2SO4, 1.0M Li2SO4, 0.1 M MES pH 6.5, protein: 0.050mL protein(10mg/mL), 0.050mL 2mM doxyTc, 0.0005mL 3M MgCl2, 100mM NaCl, 50mM Tris pH 8.0, 371 protein/precipitant
Crystal Properties
Matthews coefficientSolvent content
2.2545.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.291α = 90
b = 68.291β = 90
c = 179.612γ = 90
Symmetry
Space GroupI 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 70mirror2007-04-19MSINGLE 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
123298.70.0721.610.441423835
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)
122.0792.80.431.93

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 REPLACEMENTTHROUGHOUT6RBL2.0531.9412593104098.610.208230.203880.25665RANDOM48.282
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]
1.481.48-2.96
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.897
r_dihedral_angle_4_deg19.757
r_dihedral_angle_3_deg15.701
r_dihedral_angle_1_deg6.39
r_long_range_B_refined6.161
r_long_range_B_other6.068
r_scangle_other4.064
r_mcangle_it3.327
r_mcangle_other3.326
r_scbond_it2.67
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.897
r_dihedral_angle_4_deg19.757
r_dihedral_angle_3_deg15.701
r_dihedral_angle_1_deg6.39
r_long_range_B_refined6.161
r_long_range_B_other6.068
r_scangle_other4.064
r_mcangle_it3.327
r_mcangle_other3.326
r_scbond_it2.67
r_scbond_other2.669
r_mcbond_it2.237
r_mcbond_other2.236
r_angle_refined_deg1.689
r_angle_other_deg1.352
r_chiral_restr0.077
r_bond_refined_d0.011
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 Atoms1569
Nucleic Acid Atoms
Solvent Atoms133
Heterogen Atoms38

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata reduction
CrystalCleardata scaling
PHASERphasing