5OVI

Ras guanine nucleotide exchange factor SOS1 (Rem-cdc25) in complex with small molecule inhibitor BAY-293 (compound 23)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2II0 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5293Protein concentration 30.7 mg/ml. Protein buffer 25 Millimolar TRIS-HCL PH 7.5, 50 millimolar NaCl, 1 millimolar DTT. Reservoir 0.1 M TRIS pH 8.5, 25 % (w/v) PEG 3350. CRYO BUFFER WAS RESERVOIR SUPPLEMENTED WITH 2 MILLIMOLAR INHIBITOR (FROM 100 MILLIMOLAR DMSO STOCK) AND 15 % (v/v) ETHYLENE GLYCOL
Crystal Properties
Matthews coefficientSolvent content
2.5451.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.476α = 90
b = 84.281β = 90
c = 175.285γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2017-03-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.91841BESSY14.1

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
12.248.0298.50.140.9845.753.711121893022041.9
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)
12.22.3399.50.6440.6741.543.79

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 REPLACEMENTTHROUGHOUT2ii02.248.0228708151198.540.212550.210620.24932RANDOM42.192
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]
1.69-2.090.4
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.167
r_dihedral_angle_3_deg14.532
r_dihedral_angle_4_deg14.019
r_long_range_B_refined5.76
r_long_range_B_other5.759
r_dihedral_angle_1_deg4.94
r_scangle_other2.971
r_mcangle_it2.574
r_mcangle_other2.574
r_scbond_it1.727
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.167
r_dihedral_angle_3_deg14.532
r_dihedral_angle_4_deg14.019
r_long_range_B_refined5.76
r_long_range_B_other5.759
r_dihedral_angle_1_deg4.94
r_scangle_other2.971
r_mcangle_it2.574
r_mcangle_other2.574
r_scbond_it1.727
r_scbond_other1.727
r_mcbond_other1.495
r_mcbond_it1.494
r_angle_refined_deg1.12
r_angle_other_deg0.882
r_chiral_restr0.061
r_bond_refined_d0.007
r_gen_planes_refined0.004
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 Atoms3870
Nucleic Acid Atoms
Solvent Atoms294
Heterogen Atoms44

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing