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Affimer K69 - KRAS protein complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4OBE 4OBE, 4N6T experimental model PDB 4N6T 4OBE, 4N6T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 291 0.1M imidazole, 0.1M MES monohydrate, 20% w/v PEG 500 MME, 10% w/v PEG 20000, 0.12M 1,6-hexanediol, 0.12M 1,2-propanediol, 0.12M 1,4-butanediol, 0.12M 1-butanol, 0.12M 2-propanol, 0.12M 1,3-propanediol
Crystal Properties Matthews coefficient Solvent content 2.29 39.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.008 α = 90 b = 168.775 β = 92.7 c = 39.653 γ = 90
Symmetry Space Group P 1 21 1
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 2020-10-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
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 1.8 168.77 100 0.072 0.078 0.03 0.999 19.3 6.9 47236 25.2
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 1.83 100 0.734 0.794 0.3 0.821 6.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 4OBE, 4N6T 1.8 84.53 44810 2378 100 0.1568 0.154 0.166 0.2097 0.2228 RANDOM 29.893
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] 1.03 -0.05 -1.21 0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.552 r_dihedral_angle_4_deg 19.798 r_dihedral_angle_3_deg 12.334 r_dihedral_angle_1_deg 6.574 r_angle_refined_deg 1.314 r_rigid_bond_restr 1.304 r_angle_other_deg 1.223 r_chiral_restr 0.052 r_bond_refined_d 0.005 r_gen_planes_refined 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.552 r_dihedral_angle_4_deg 19.798 r_dihedral_angle_3_deg 12.334 r_dihedral_angle_1_deg 6.574 r_angle_refined_deg 1.314 r_rigid_bond_restr 1.304 r_angle_other_deg 1.223 r_chiral_restr 0.052 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4253 Nucleic Acid Atoms Solvent Atoms 258 Heterogen Atoms 58
Software Software Software Name Purpose DIALS data scaling PHASER phasing REFMAC refinement DIALS data reduction