3IQU

Crystal Structure of human 14-3-3 sigma in Complex with Raf1 peptide (6mer)


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
2.6553.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.18α = 90
b = 112.17β = 90
c = 62.73γ = 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 Sym 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
11.0534.0399.10.05514.85.5134589133400-3-312.532
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)
11.051.197.50.3973.916942

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 REPLACEMENTTHROUGHOUT1YWT1.0525126774662199.120.129710.128570.1509RANDOM9.982
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]
0.080.9-0.98
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.404
r_dihedral_angle_4_deg16.048
r_sphericity_free15.637
r_dihedral_angle_3_deg13.546
r_dihedral_angle_1_deg12.089
r_sphericity_bonded6.764
r_scangle_it6.741
r_scbond_it4.901
r_mcangle_it3.108
r_rigid_bond_restr2.464
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.404
r_dihedral_angle_4_deg16.048
r_sphericity_free15.637
r_dihedral_angle_3_deg13.546
r_dihedral_angle_1_deg12.089
r_sphericity_bonded6.764
r_scangle_it6.741
r_scbond_it4.901
r_mcangle_it3.108
r_rigid_bond_restr2.464
r_angle_refined_deg2.198
r_mcbond_it2.113
r_angle_other_deg1.159
r_mcbond_other1.074
r_chiral_restr0.16
r_bond_refined_d0.028
r_gen_planes_refined0.011
r_bond_other_d0.004
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 Atoms1909
Nucleic Acid Atoms
Solvent Atoms492
Heterogen Atoms4

Software

Software
Software NamePurpose
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling