5OVG

Ras guanine nucleotide exchange factor SOS1 (Rem-cdc25) in complex with small molecule inhibitor compound 18


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5293Protein concentration 30.7 mg/ml. Protein buffer 25 Millimolar TRIS-HCL PH 7.5, 50 millimolar NaCl, 1 millimolar DTT. Reservoir 27% (v/v) ethylenglycol. Protein incubated with 2 MILLIMOLAR LIGAND prior to crystallization.
Crystal Properties
Matthews coefficientSolvent content
2.754.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.984α = 90
b = 85.671β = 90
c = 176.79γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2015-06-25MSINGLE 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
12.348.5599.40.0970.99711.644.322853247.1
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)
12.32.4499.10.6350.8321.934.47

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 REPLACEMENTTHROUGHOUT2ii02.348.5527105142799.440.244110.241260.29696RANDOM55.688
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]
4.94-1.16-3.78
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.229
r_dihedral_angle_3_deg14.777
r_dihedral_angle_4_deg11.987
r_long_range_B_refined9.547
r_long_range_B_other9.546
r_scangle_other6.702
r_mcangle_it6.386
r_mcangle_other6.385
r_dihedral_angle_1_deg4.897
r_scbond_it4.057
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.229
r_dihedral_angle_3_deg14.777
r_dihedral_angle_4_deg11.987
r_long_range_B_refined9.547
r_long_range_B_other9.546
r_scangle_other6.702
r_mcangle_it6.386
r_mcangle_other6.385
r_dihedral_angle_1_deg4.897
r_scbond_it4.057
r_mcbond_it4.05
r_scbond_other4.05
r_mcbond_other4.047
r_angle_refined_deg1.121
r_angle_other_deg0.874
r_chiral_restr0.059
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 Atoms3786
Nucleic Acid Atoms
Solvent Atoms239
Heterogen Atoms39

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing