8CNJ

HRas(1-166) in complex with GDP and BeF3-


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP277BeF3- GSA complexes were obtained under vapour diffusion sitting drop conditions. Protein buffer (HRas pY64 or HRas 0.4 mM, Na-HEPES 20 mM pH = 8.0, MgCl2 5 mM, NaF 20 mM) were mixed with precipitant in a 1:1 ratio with a total drop size of 600 nL. The precipitant solution consited of: (30 % (v/v) MPD, 100 mM imidazole, pH = 7.0). Protein crystals were soaked in their respective precipitant solutions containing 50 mM BeCl2 and subsequently flash-frozen using 20% glycerol as cryoprotectant.
Crystal Properties
Matthews coefficientSolvent content
2.1342.32

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.433α = 90
b = 51.957β = 90
c = 136.149γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 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)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
11.3551.9696.20.0930.10.0380.99913.712.669077
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)
11.351.371.5321.7120.7430.5988.6

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-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.3548.58968993354896.2220.1450.14320.1791RANDOM18.638
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]
1.7510.154-1.905
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg16.511
r_dihedral_angle_3_deg12.421
r_dihedral_angle_2_deg8.076
r_dihedral_angle_1_deg6.23
r_rigid_bond_restr2.674
r_lrange_it2.526
r_lrange_other2.196
r_scangle_it1.417
r_scangle_other1.417
r_angle_refined_deg1.412
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg16.511
r_dihedral_angle_3_deg12.421
r_dihedral_angle_2_deg8.076
r_dihedral_angle_1_deg6.23
r_rigid_bond_restr2.674
r_lrange_it2.526
r_lrange_other2.196
r_scangle_it1.417
r_scangle_other1.417
r_angle_refined_deg1.412
r_mcangle_it1.267
r_mcangle_other1.267
r_scbond_other0.998
r_scbond_it0.997
r_mcbond_it0.84
r_mcbond_other0.839
r_angle_other_deg0.47
r_nbd_refined0.225
r_chiral_restr0.219
r_symmetry_nbd_other0.184
r_nbtor_refined0.178
r_nbd_other0.154
r_xyhbond_nbd_refined0.135
r_symmetry_xyhbond_nbd_refined0.13
r_symmetry_nbd_refined0.123
r_symmetry_nbtor_other0.076
r_dihedral_angle_other_2_deg0.06
r_bond_refined_d0.011
r_gen_planes_refined0.007
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2644
Nucleic Acid Atoms
Solvent Atoms255
Heterogen Atoms74

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing