8BOS

Transition state analogue complex of small G protein and its GAP effector


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1WQ1 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8293precipitant: HEPES-Na 100 mM pH = 8.0, PEG3350 22% (w/v), (NH4)2SO4 20 mM, Gd-HCl 100 mM, NaF 20 mM protein buffer: HRas 0.400 mM, RasGAP 0.400 mM, HEPES-Na 20 mM, NaF 20 mM drop size: 5 uL, protein:precipitant ratio: 1:1.2
Crystal Properties
Matthews coefficientSolvent content
2.2645.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.832α = 90
b = 41.558β = 109.25
c = 89.674γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 16M2021-03-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.976DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
12.184.6654.10.1760.2130.1120.98112.63.416248
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.160.6590.8210.4780.5521.72.8

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 REPLACEMENTTHROUGHOUT1WQ12.184.661545279154.810.202170.198020.27994RANDOM43.913
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]
-0.280.040.020.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg18.398
r_long_range_B_refined7.971
r_long_range_B_other7.971
r_dihedral_angle_1_deg7.299
r_dihedral_angle_2_deg5.693
r_scangle_other5.381
r_mcangle_other4.94
r_mcangle_it4.939
r_scbond_it3.516
r_scbond_other3.513
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg18.398
r_long_range_B_refined7.971
r_long_range_B_other7.971
r_dihedral_angle_1_deg7.299
r_dihedral_angle_2_deg5.693
r_scangle_other5.381
r_mcangle_other4.94
r_mcangle_it4.939
r_scbond_it3.516
r_scbond_other3.513
r_mcbond_it3.218
r_mcbond_other3.205
r_angle_refined_deg1.437
r_angle_other_deg0.46
r_chiral_restr0.06
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
r_dihedral_angle_4_deg
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 Atoms3914
Nucleic Acid Atoms
Solvent Atoms58
Heterogen Atoms1

Software

Software
Software NamePurpose
REFMACrefinement
Cootmodel building
Aimlessdata scaling
MOLREPphasing
xia2data reduction