5OVD

Ras guanine nucleotide exchange factor SOS1 (Rem-cdc25) in new crystal form


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. No cryo required as grown from ethylenglycol as precipitant
Crystal Properties
Matthews coefficientSolvent content
2.6854.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.941α = 90
b = 85.372β = 90
c = 176.1γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2017-08-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.9184BESSY14.1

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
11.948.3798.70.060.99913.994.794929743.44
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)
11.92.0197.61.0520.6781.464.87

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 REPLACEMENTTHROUGHOUT2ii01.948.3747196210198.720.200440.198660.24022RANDOM54.861
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]
1.98-2.370.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.024
r_dihedral_angle_4_deg15.951
r_dihedral_angle_3_deg14.565
r_long_range_B_refined7.257
r_long_range_B_other7.256
r_dihedral_angle_1_deg5.044
r_scangle_other3.694
r_scbond_it2.455
r_scbond_other2.448
r_mcangle_other2.257
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.024
r_dihedral_angle_4_deg15.951
r_dihedral_angle_3_deg14.565
r_long_range_B_refined7.257
r_long_range_B_other7.256
r_dihedral_angle_1_deg5.044
r_scangle_other3.694
r_scbond_it2.455
r_scbond_other2.448
r_mcangle_other2.257
r_mcangle_it2.254
r_mcbond_it1.533
r_mcbond_other1.517
r_angle_refined_deg1.295
r_angle_other_deg0.933
r_chiral_restr0.076
r_bond_refined_d0.01
r_gen_planes_refined0.006
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 Atoms3856
Nucleic Acid Atoms
Solvent Atoms344
Heterogen Atoms20

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing