8T5M

SOS2 crystal structure with fragment bound (compound 14)


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% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.5652.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.471α = 85.05
b = 52.165β = 75.37
c = 60.998γ = 76.21
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9M2022-03-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08ID-11.0332CLSI08ID-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
11.7943.8291.20.9910.093.546269
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)
11.791.840.32

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 REPLACEMENTTHROUGHOUT1.7943.8244042222591.280.191870.190030.22792RANDOM36.392
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]
0.87-0.13-0.15-0.06-1.39-0.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.164
r_dihedral_angle_3_deg17.181
r_dihedral_angle_4_deg15.821
r_long_range_B_refined7.627
r_long_range_B_other7.626
r_dihedral_angle_1_deg6.167
r_scangle_other5.842
r_mcangle_it4.046
r_mcangle_other4.045
r_scbond_it3.797
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.164
r_dihedral_angle_3_deg17.181
r_dihedral_angle_4_deg15.821
r_long_range_B_refined7.627
r_long_range_B_other7.626
r_dihedral_angle_1_deg6.167
r_scangle_other5.842
r_mcangle_it4.046
r_mcangle_other4.045
r_scbond_it3.797
r_scbond_other3.796
r_mcbond_it2.888
r_mcbond_other2.86
r_angle_refined_deg1.458
r_angle_other_deg1.319
r_chiral_restr0.078
r_bond_refined_d0.008
r_gen_planes_refined0.007
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 Atoms3847
Nucleic Acid Atoms
Solvent Atoms210
Heterogen Atoms49

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
Cootmodel building