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HRas(1-166) in complex with GDP and BeF3-
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 BeF3- 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 coefficient Solvent content 2.13 42.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.433 α = 90 b = 51.957 β = 90 c = 136.149 γ = 90
Symmetry Space Group P 21 21 21
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 X 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) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.35 51.96 96.2 0.093 0.1 0.038 0.999 13.7 12.6 69077
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) Redundancy Number Unique Reflections (All) 1 1.35 1.37 1.532 1.712 0.743 0.598 8.6
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.35 48.589 68993 3548 96.222 0.145 0.1432 0.1791 0.1944 RANDOM 18.638
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] 1.751 0.154 -1.905
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.511 r_dihedral_angle_3_deg 12.421 r_dihedral_angle_2_deg 8.076 r_dihedral_angle_1_deg 6.23 r_rigid_bond_restr 2.674 r_lrange_it 2.526 r_lrange_other 2.196 r_scangle_it 1.417 r_scangle_other 1.417 r_angle_refined_deg 1.412
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.511 r_dihedral_angle_3_deg 12.421 r_dihedral_angle_2_deg 8.076 r_dihedral_angle_1_deg 6.23 r_rigid_bond_restr 2.674 r_lrange_it 2.526 r_lrange_other 2.196 r_scangle_it 1.417 r_scangle_other 1.417 r_angle_refined_deg 1.412 r_mcangle_it 1.267 r_mcangle_other 1.267 r_scbond_other 0.998 r_scbond_it 0.997 r_mcbond_it 0.84 r_mcbond_other 0.839 r_angle_other_deg 0.47 r_nbd_refined 0.225 r_chiral_restr 0.219 r_symmetry_nbd_other 0.184 r_nbtor_refined 0.178 r_nbd_other 0.154 r_xyhbond_nbd_refined 0.135 r_symmetry_xyhbond_nbd_refined 0.13 r_symmetry_nbd_refined 0.123 r_symmetry_nbtor_other 0.076 r_dihedral_angle_other_2_deg 0.06 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2644 Nucleic Acid Atoms Solvent Atoms 255 Heterogen Atoms 74
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling MOLREP phasing