6EIE

Ras guanine nucleotide exchange factor SOS2 (Rem-cdc25), with surface mutations


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP293Protein 10.3 mg/ml in 25 mM Tris HCl, pH 7.5, 100 mM NaCl, 1 mM DTT. Reservoir 0,1 M Natriumacetat, 20% w/v PEG 3350. Cryo buffer was reservoir supplemented with 15% glycerol.
Crystal Properties
Matthews coefficientSolvent content
2.3347.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.97α = 90
b = 53.97β = 90
c = 183.793γ = 90
Symmetry
Space GroupP 43

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2016-05-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, DESY BEAMLINE P111.0332PETRA III, DESYP11

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)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
12.7246.5496.90.0670.99814.14.81364469.7
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.722.8882.70.5390.7613.2

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 REPLACEMENTTHROUGHOUT1NVU2.7246.541296068396.940.221710.218360.28526RANDOM79.654
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]
-6.06-6.0612.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.999
r_dihedral_angle_3_deg17.663
r_dihedral_angle_4_deg15.263
r_long_range_B_refined7.026
r_long_range_B_other7.026
r_dihedral_angle_1_deg6.278
r_mcangle_it4.737
r_mcangle_other4.736
r_scangle_other4.562
r_mcbond_other2.793
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.999
r_dihedral_angle_3_deg17.663
r_dihedral_angle_4_deg15.263
r_long_range_B_refined7.026
r_long_range_B_other7.026
r_dihedral_angle_1_deg6.278
r_mcangle_it4.737
r_mcangle_other4.736
r_scangle_other4.562
r_mcbond_other2.793
r_mcbond_it2.792
r_scbond_it2.554
r_scbond_other2.553
r_angle_refined_deg1.244
r_angle_other_deg0.951
r_chiral_restr0.071
r_bond_refined_d0.008
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 Atoms3793
Nucleic Acid Atoms
Solvent Atoms8
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing