3IQJ

Crystal Structure of human 14-3-3 sigma in Complex with Raf1 peptide (10mer)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1YWT 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52770.1M Hepes/NaOH ph 7.5, 0.2M CaCl2, 28% PEG 400, 5% glycerol, 2mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.6253.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.61α = 90
b = 112.56β = 90
c = 62.68γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2009-03-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.87314SLSX10SA

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
11.1534.4999.40.05815.26.2103535102954-3-315.78
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.151.20.4693.84.712259

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 REPLACEMENTTHROUGHOUT1YWT1.1534.4997849510599.440.128560.127250.15267RANDOM11.535
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]
0.32-0.29-0.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.694
r_dihedral_angle_4_deg16.528
r_sphericity_free15.853
r_dihedral_angle_1_deg14.475
r_dihedral_angle_3_deg11.348
r_scangle_it7.061
r_sphericity_bonded6.352
r_scbond_it5.08
r_mcangle_it3.492
r_rigid_bond_restr2.556
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.694
r_dihedral_angle_4_deg16.528
r_sphericity_free15.853
r_dihedral_angle_1_deg14.475
r_dihedral_angle_3_deg11.348
r_scangle_it7.061
r_sphericity_bonded6.352
r_scbond_it5.08
r_mcangle_it3.492
r_rigid_bond_restr2.556
r_mcbond_it2.389
r_angle_refined_deg2.14
r_mcbond_other1.144
r_angle_other_deg1.116
r_chiral_restr0.145
r_bond_refined_d0.027
r_gen_planes_refined0.011
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1895
Nucleic Acid Atoms
Solvent Atoms429
Heterogen Atoms4

Software

Software
Software NamePurpose
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling