5OVF

Ras guanine nucleotide exchange factor SOS1 (Rem-cdc25) in complex with small molecule inhibitor compound 17


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherINHOUSE STRUCTURE

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 27% (v/v) ethylenglycol. Protein incubated with 2 MILLIMOLAR LIGAND prior to crystallization.
Crystal Properties
Matthews coefficientSolvent content
2.6152.93

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.895α = 90
b = 85.161β = 90
c = 176.537γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 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
12.0148.4199.30.1120.99810.834.364098235.65
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)
12.012.1398.30.790.6651.874.33

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 REPLACEMENTTHROUGHOUTINHOUSE STRUCTURE2.0148.4138932205099.30.248290.246350.28501RANDOM35.94
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]
3.49-2.35-1.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.959
r_dihedral_angle_4_deg15.743
r_dihedral_angle_3_deg13.714
r_long_range_B_refined6.135
r_long_range_B_other6.135
r_dihedral_angle_1_deg4.663
r_scangle_other3.74
r_mcangle_it3.167
r_mcangle_other3.167
r_scbond_it2.204
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.959
r_dihedral_angle_4_deg15.743
r_dihedral_angle_3_deg13.714
r_long_range_B_refined6.135
r_long_range_B_other6.135
r_dihedral_angle_1_deg4.663
r_scangle_other3.74
r_mcangle_it3.167
r_mcangle_other3.167
r_scbond_it2.204
r_scbond_other2.203
r_mcbond_it1.956
r_mcbond_other1.956
r_angle_refined_deg1.042
r_angle_other_deg0.863
r_chiral_restr0.056
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 Atoms3910
Nucleic Acid Atoms
Solvent Atoms293
Heterogen Atoms33

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing