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BeF3 Phospho-HRas GSA complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QRA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 Protein 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 coefficient Solvent content 2.52 51.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.77 α = 90 b = 87.77 β = 90 c = 132.381 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER2 S 16M 2023-02-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.48 49.92 100 1 15.8 20.3 32936
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.48 1.51 100 0.559 1.2 20.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.48 44.17 31254 1679 99.99 0.16509 0.16384 0.1715 0.18838 0.1923 RANDOM 22.508
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 -0.15 0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 13.174 r_dihedral_angle_3_deg 12.621 r_long_range_B_refined 7.393 r_long_range_B_other 7.213 r_scangle_other 5.945 r_dihedral_angle_1_deg 5.798 r_scbond_it 4.076 r_scbond_other 3.99 r_mcangle_other 2.826 r_mcangle_it 2.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 13.174 r_dihedral_angle_3_deg 12.621 r_long_range_B_refined 7.393 r_long_range_B_other 7.213 r_scangle_other 5.945 r_dihedral_angle_1_deg 5.798 r_scbond_it 4.076 r_scbond_other 3.99 r_mcangle_other 2.826 r_mcangle_it 2.82 r_mcbond_it 2.08 r_mcbond_other 2.009 r_angle_refined_deg 1.816 r_angle_other_deg 0.923 r_chiral_restr 0.222 r_bond_refined_d 0.015 r_gen_planes_other 0.013 r_gen_planes_refined 0.01 r_bond_other_d 0.002 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 Atoms Number Protein Atoms 1385 Nucleic Acid Atoms Solvent Atoms 123 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling MOLREP phasing Coot model building