X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP277Protein buffer (phospho-HRas pY64 0.4 mM, RasGAP 0.4 mM, Na-HEPES 20 mM pH = 8.0, MgCl2 5 mM, NaF 20 mM) was mixed with precipitant in a 1:1 ratio with a total drop size of 600 nL. The precipitant solution consits of: 100 mM NaOAc, pH = 4.5, 200 mM Li2SO4, 50% PEG400 (v/v). Protein crystals were soaked in precipitant solutions containing 50-100 mM BeCl2 and subsequently flash-frozen using 20% glycerol as cryoprotectant.
Crystal Properties
Matthews coefficientSolvent content
2.5251.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.77α = 90
b = 87.77β = 90
c = 132.381γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 S 16M2023-02-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9763DiamondI03

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
11.4849.92100115.820.332936
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)
11.481.511000.5591.220.4

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 REPLACEMENTTHROUGHOUT1.4844.1731254167999.990.165090.163840.18838RANDOM22.508
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]
-0.15-0.07-0.150.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg13.174
r_dihedral_angle_3_deg12.621
r_long_range_B_refined7.393
r_long_range_B_other7.213
r_scangle_other5.945
r_dihedral_angle_1_deg5.798
r_scbond_it4.076
r_scbond_other3.99
r_mcangle_other2.826
r_mcangle_it2.82
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg13.174
r_dihedral_angle_3_deg12.621
r_long_range_B_refined7.393
r_long_range_B_other7.213
r_scangle_other5.945
r_dihedral_angle_1_deg5.798
r_scbond_it4.076
r_scbond_other3.99
r_mcangle_other2.826
r_mcangle_it2.82
r_mcbond_it2.08
r_mcbond_other2.009
r_angle_refined_deg1.816
r_angle_other_deg0.923
r_chiral_restr0.222
r_bond_refined_d0.015
r_gen_planes_other0.013
r_gen_planes_refined0.01
r_bond_other_d0.002
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 Atoms1385
Nucleic Acid Atoms
Solvent Atoms123
Heterogen Atoms16

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing
Cootmodel building