X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293Using a commercial crystal screen (HAMPTON RESEARCH, HR2-130) yielded a hit for monophosphorylated HRas under sitting drop conditions (drop size 600 nL) with a 1:1 ratio of protein solution (phospho-HRas 0.4 mM, RasGAP 0.4 mM, Na-HEPES 20 mM pH = 8.0, MgCl2 5 mM, NaF 20 mM) and precipitant (Na-citrate 100 mM pH = 5.6, Li2SO4 1.0 M, CaCl2 200 mM). After three rounds of microseeding well-formed single crystals were obtained using 2.0 uL sitting drops and a 1:1 ratio of protein buffer (HRas 400 uM, RasGAP 400 uM, MgCl2 5 mM, Na-HEPES 20 mM pH = 8.0, NaF 20 mM) and precipitant (Na-Citrate 100 mM pH = 5.6, Li2SO4 800 mM, CaCl2 200 mM). These were harvested using cryoprotectant (80% precipitant, 20% glycerol (v/v)) and sent for data collection.
Crystal Properties
Matthews coefficientSolvent content
2.6152.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.662α = 90
b = 92.662β = 90
c = 119.323γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 16M2021-01-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9763DiamondI03

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
11.3247.92599.20.0410.0430.014128.617.645988
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)
11.321.341.341.5350.7230.5777.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1.3247.92545983223299.1760.1370.13540.173922.946
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]
-0.796-0.398-0.7962.583
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg16.648
r_rigid_bond_restr15.682
r_dihedral_angle_3_deg14.448
r_dihedral_angle_2_deg8.675
r_scbond_other7.62
r_scbond_it7.604
r_scangle_it7.202
r_scangle_other7.192
r_dihedral_angle_1_deg6.465
r_lrange_it5.369
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg16.648
r_rigid_bond_restr15.682
r_dihedral_angle_3_deg14.448
r_dihedral_angle_2_deg8.675
r_scbond_other7.62
r_scbond_it7.604
r_scangle_it7.202
r_scangle_other7.192
r_dihedral_angle_1_deg6.465
r_lrange_it5.369
r_lrange_other5.079
r_mcangle_it3.612
r_mcangle_other3.61
r_mcbond_it3.283
r_mcbond_other3.171
r_angle_refined_deg1.607
r_angle_other_deg0.592
r_nbd_refined0.266
r_xyhbond_nbd_refined0.222
r_symmetry_nbd_other0.201
r_nbtor_refined0.18
r_symmetry_xyhbond_nbd_refined0.174
r_symmetry_nbd_refined0.163
r_nbd_other0.147
r_chiral_restr0.089
r_symmetry_nbtor_other0.083
r_bond_refined_d0.01
r_gen_planes_refined0.009
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1280
Nucleic Acid Atoms
Solvent Atoms128
Heterogen Atoms34

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
DIALSdata reduction
MOLREPphasing
Cootmodel building