5OVH

Ras guanine nucleotide exchange factor SOS1 (Rem-cdc25) in complex with small molecule inhibitor compound 21


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5293Protein concentration 30.7 mg/ml. Protein buffer 25 Millimolar TRIS-HCL PH 7.5, 50 millimolar NaCl, 1 millimolar DTT. Reservoir 23% (v/v) ethylenglycol. Protein incubated with 5 MILLIMOLAR LIGAND overnight at 277K prior to crystallization.
Crystal Properties
Matthews coefficientSolvent content
2.7154.69

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.413α = 90
b = 85.362β = 90
c = 176.221γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2015-08-20MSINGLE 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
12.348.499.50.0510.99922.135.32856045.4
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)
12.32.4498.80.3280.944.865.33

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 REPLACEMENTTHROUGHOUT2ii02.344.0627149142999.590.263240.259690.33022RANDOM49.569
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]
3.86-1.98-1.88
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.787
r_dihedral_angle_3_deg14.43
r_dihedral_angle_4_deg11.681
r_long_range_B_refined7.712
r_long_range_B_other7.711
r_scangle_other5.229
r_mcangle_it5.123
r_mcangle_other5.122
r_dihedral_angle_1_deg4.828
r_mcbond_it3.229
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.787
r_dihedral_angle_3_deg14.43
r_dihedral_angle_4_deg11.681
r_long_range_B_refined7.712
r_long_range_B_other7.711
r_scangle_other5.229
r_mcangle_it5.123
r_mcangle_other5.122
r_dihedral_angle_1_deg4.828
r_mcbond_it3.229
r_mcbond_other3.223
r_scbond_it3.17
r_scbond_other3.167
r_angle_refined_deg1.098
r_angle_other_deg0.863
r_chiral_restr0.058
r_bond_refined_d0.007
r_gen_planes_refined0.003
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 Atoms3778
Nucleic Acid Atoms
Solvent Atoms316
Heterogen Atoms39

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing