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The crystal structure of human abl1 kinase domain in complex with PH-ELV-1022
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QOH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 289 100 mM MES pH 6.0, 25 mM magnesium formate, 30% PEG 4000, 4% ethylene glycol
Crystal Properties Matthews coefficient Solvent content 3.11 60.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.291 α = 90 b = 117.277 β = 90 c = 126.36 γ = 90
Symmetry Space Group P 2 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 PILATUS 6M 2024-12-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL14-1 1.19499 SSRL BL14-1
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 2.6 126.33 97.6 0.514 0.539 0.159 0.962 3.5 10.8 25755
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.72 98.1 2.706 0.83 0.316 0.8 11
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 2.6 63.26 24346 1337 96.94 0.25285 0.25111 0.256 0.2846 0.2904 RANDOM 45.23
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] -1.33 2.04 -0.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.933 r_dihedral_angle_3_deg 17.791 r_long_range_B_refined 8.484 r_long_range_B_other 8.479 r_scangle_other 6.005 r_dihedral_angle_1_deg 5.449 r_mcangle_it 5.333 r_mcangle_other 5.332 r_scbond_it 3.672 r_scbond_other 3.671
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.933 r_dihedral_angle_3_deg 17.791 r_long_range_B_refined 8.484 r_long_range_B_other 8.479 r_scangle_other 6.005 r_dihedral_angle_1_deg 5.449 r_mcangle_it 5.333 r_mcangle_other 5.332 r_scbond_it 3.672 r_scbond_other 3.671 r_mcbond_it 3.346 r_mcbond_other 3.346 r_angle_refined_deg 1.402 r_angle_other_deg 0.572 r_chiral_restr 0.071 r_bond_refined_d 0.009 r_bond_other_d 0.004 r_gen_planes_refined 0.004 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 4318 Nucleic Acid Atoms Solvent Atoms 105 Heterogen Atoms 94
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction DIALS data reduction Aimless data scaling PHASER phasing PHENIX refinement