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Crystal structure of HRAS in complex with N-LHY affibody
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.3 289 0.2 M AMMONIUM NITRATE, 20 % (W/V) PEG3350
Crystal Properties Matthews coefficient Solvent content 1.31 6.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.529 α = 90 b = 55.529 β = 90 c = 280.68 γ = 120
Symmetry Space Group P 61 2 2
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 EIGER X 9M 2025-06-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 19-ID 0.97860 NSLS-II 19-ID
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 1.8 280.64 100 0.106 0.107 0.018 0.999 20.7 34.5 25123 36.6
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 1.8 1.83 97.7 3.437 3.539 0.815 0.543 19.9
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 1.8 48.09 23192 1738 99.47 0.20382 0.2023 0.2024 0.22385 0.2234 RANDOM 48.276
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] 0.24 0.12 0.24 -0.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.554 r_long_range_B_refined 7.575 r_long_range_B_other 7.566 r_dihedral_angle_2_deg 7.474 r_dihedral_angle_1_deg 6.264 r_scangle_other 6.178 r_scbond_it 4.099 r_scbond_other 4.096 r_mcangle_it 3.82 r_mcangle_other 3.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.554 r_long_range_B_refined 7.575 r_long_range_B_other 7.566 r_dihedral_angle_2_deg 7.474 r_dihedral_angle_1_deg 6.264 r_scangle_other 6.178 r_scbond_it 4.099 r_scbond_other 4.096 r_mcangle_it 3.82 r_mcangle_other 3.82 r_mcbond_it 2.73 r_mcbond_other 2.723 r_angle_refined_deg 1.84 r_angle_other_deg 0.623 r_chiral_restr 0.084 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 1622 Nucleic Acid Atoms Solvent Atoms 87 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement PHENIX refinement xia2 data reduction xia2 data scaling MOLREP phasing