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Structure of Human ROS1 Kinase Domain Harboring the G2032R Solvent-front Mutation in Complex with Zidesamtinib (NVL-520)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4UXL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.83 285 0.6 M Potassium Thiocyanate, 0.1 M Citric Acid/Tri-sodium Citrate pH 4.83, 22% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.37 48.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.02 α = 90 b = 106.02 β = 90 c = 50.51 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 X CdTe 16M 2024-01-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.885603 ESRF ID23-1
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 2.205 34.703 73.4 0.086 0.093 0.034 0.998 11.2 7.6 12138 78.4
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 2.205 2.427 29.7 1.373 1.495 0.585 0.671 1.5 6.4
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS FREE R-VALUE 2.205 34.703 12137 370 73.375 0.203 0.2011 0.2066 0.2722 0.2788 66.337
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] 0.562 0.281 0.562 -1.823
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.922 r_dihedral_angle_6_deg 11.234 r_lrange_other 6.417 r_lrange_it 6.416 r_dihedral_angle_1_deg 5.749 r_scangle_it 3.948 r_scangle_other 3.946 r_dihedral_angle_2_deg 3.917 r_mcangle_it 3.672 r_mcangle_other 3.671
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.922 r_dihedral_angle_6_deg 11.234 r_lrange_other 6.417 r_lrange_it 6.416 r_dihedral_angle_1_deg 5.749 r_scangle_it 3.948 r_scangle_other 3.946 r_dihedral_angle_2_deg 3.917 r_mcangle_it 3.672 r_mcangle_other 3.671 r_scbond_it 2.32 r_scbond_other 2.32 r_mcbond_it 2.198 r_mcbond_other 2.198 r_angle_refined_deg 0.981 r_angle_other_deg 0.327 r_nbd_refined 0.203 r_symmetry_nbd_other 0.178 r_nbtor_refined 0.174 r_symmetry_xyhbond_nbd_refined 0.168 r_nbd_other 0.149 r_xyhbond_nbd_refined 0.146 r_symmetry_nbd_refined 0.102 r_symmetry_nbtor_other 0.075 r_symmetry_xyhbond_nbd_other 0.063 r_chiral_restr 0.043 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2217 Nucleic Acid Atoms Solvent Atoms 42 Heterogen Atoms 35
Software Software Software Name Purpose XDS data reduction Aimless data scaling STARANISO data scaling PHASER phasing REFMAC refinement