8T5R

SOS2 crystal structure with fragment bound (compound 13)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherUsed apo as initial model

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP281.1510% PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.4148.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.396α = 84.97
b = 52.008β = 75.59
c = 60.918γ = 76.07
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2022-03-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08B1-11.1808CLSI08B1-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.1243.895.50.998.52329014
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.122.180.280.72

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.1243.827579143695.490.215270.212310.27192RANDOM46.848
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]
0.45-0.31-0.50.36-1.22-1.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.815
r_dihedral_angle_3_deg18.903
r_dihedral_angle_4_deg17.181
r_long_range_B_refined8.724
r_long_range_B_other8.723
r_dihedral_angle_1_deg7.066
r_scangle_other6.746
r_mcangle_other5.939
r_mcangle_it5.937
r_scbond_it4.699
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.815
r_dihedral_angle_3_deg18.903
r_dihedral_angle_4_deg17.181
r_long_range_B_refined8.724
r_long_range_B_other8.723
r_dihedral_angle_1_deg7.066
r_scangle_other6.746
r_mcangle_other5.939
r_mcangle_it5.937
r_scbond_it4.699
r_scbond_other4.698
r_mcbond_it4.155
r_mcbond_other4.153
r_angle_refined_deg1.576
r_angle_other_deg1.285
r_chiral_restr0.079
r_bond_refined_d0.009
r_gen_planes_refined0.008
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 Atoms3815
Nucleic Acid Atoms
Solvent Atoms63
Heterogen Atoms22

Software

Software
Software NamePurpose
REFMACrefinement
autoPROCdata processing
XSCALEdata scaling
Cootmodel building