6YOX

14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound TCF521-027


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2770.095 M HEPES Na pH 7.1, 27% PEG400, 0.19M Calcium chloride, 5% Glycerol
Crystal Properties
Matthews coefficientSolvent content
2.4549.78

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.148α = 90
b = 111.89β = 90
c = 62.269γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2018-12-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I240.91587DiamondI24

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)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
12.0562.281000.260.2720.994611.618437
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)R Split (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.052.11000.951.0140.8871.8

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 REPLACEMENTFREE R-VALUE6QHL2.0556.011752589899.920.195370.192760.24518RANDOM31.937
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]
1.341.95-3.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.625
r_dihedral_angle_3_deg13.941
r_dihedral_angle_4_deg12.832
r_long_range_B_refined5.822
r_long_range_B_other5.619
r_dihedral_angle_1_deg5.327
r_scangle_other4.187
r_mcangle_other3.371
r_mcangle_it3.364
r_scbond_it2.718
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.625
r_dihedral_angle_3_deg13.941
r_dihedral_angle_4_deg12.832
r_long_range_B_refined5.822
r_long_range_B_other5.619
r_dihedral_angle_1_deg5.327
r_scangle_other4.187
r_mcangle_other3.371
r_mcangle_it3.364
r_scbond_it2.718
r_scbond_other2.717
r_mcbond_it2.217
r_mcbond_other2.184
r_angle_refined_deg1.197
r_angle_other_deg0.947
r_chiral_restr0.064
r_bond_refined_d0.009
r_gen_planes_refined0.005
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 Atoms1899
Nucleic Acid Atoms
Solvent Atoms230
Heterogen Atoms14

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing