8T5G

SOS2 co-crystal structure with fragment bound (compound 12)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6EIE 

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 = 46.576α = 84.84
b = 52.339β = 75.48
c = 60.932γ = 75.95
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
11.9243.9970.998.433.640046
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)
11.921.970.27

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 REPLACEMENTTHROUGHOUT6EIE1.9243.938129191997.040.200390.198350.24032RANDOM39.152
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]
0.98-0.110.120.37-1.21-1.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.139
r_dihedral_angle_4_deg17.997
r_dihedral_angle_3_deg17.608
r_long_range_B_refined8.661
r_long_range_B_other8.66
r_dihedral_angle_1_deg6.4
r_scangle_other5.876
r_mcangle_it4.338
r_mcangle_other4.337
r_scbond_it3.866
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.139
r_dihedral_angle_4_deg17.997
r_dihedral_angle_3_deg17.608
r_long_range_B_refined8.661
r_long_range_B_other8.66
r_dihedral_angle_1_deg6.4
r_scangle_other5.876
r_mcangle_it4.338
r_mcangle_other4.337
r_scbond_it3.866
r_scbond_other3.865
r_mcbond_other3.083
r_mcbond_it3.082
r_angle_refined_deg1.462
r_angle_other_deg1.292
r_chiral_restr0.072
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 Atoms3839
Nucleic Acid Atoms
Solvent Atoms202
Heterogen Atoms39

Software

Software
Software NamePurpose
REFMACrefinement
autoPROCdata processing
XSCALEdata scaling
Cootmodel building