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Identification of an intermediate activation state of PAK5 reveals a novel mechanism of kinase inhibition.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2F57 experimental model PDB 6YXW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291 0.12 M Alcohols (0.2 M 1,6-Hexanediol, 0.2 M 1-Butanol, 0.2 M 1,2_Propanediol, 0.2 M 2-Propanol, 0.2 M 1,4-Butanediol, 0.2 M 1,3-Propanediol), 0.1 M Buffer System 2 (1.0 M Sodium HEPES, MOPS) pH 7.5, 37.5% precipitant (M1K3350)
Crystal Properties Matthews coefficient Solvent content 2.47 50.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.355 α = 90 b = 58.313 β = 90 c = 129.472 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 XE 16M 2022-02-03 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 1.549 53.17 100 0.056 0.059 0.016 0.999 16.3 13.4 64001 28.7
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 1.55 1.58 97.8 2.812 2.922 0.783 0.577 13.4
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 MOLECULAR REPLACEMENT FREE R-VALUE 1.549 53.169 63911 3170 99.872 0.199 0.1972 0.2 0.2341 0.2362 40.435
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] -1.668 3.318 -1.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.716 r_dihedral_angle_3_deg 13.153 r_dihedral_angle_4_deg 13.029 r_dihedral_angle_1_deg 6.109 r_lrange_it 2.945 r_lrange_other 2.812 r_scangle_it 2.043 r_scangle_other 2.043 r_mcangle_it 1.997 r_mcangle_other 1.997
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.716 r_dihedral_angle_3_deg 13.153 r_dihedral_angle_4_deg 13.029 r_dihedral_angle_1_deg 6.109 r_lrange_it 2.945 r_lrange_other 2.812 r_scangle_it 2.043 r_scangle_other 2.043 r_mcangle_it 1.997 r_mcangle_other 1.997 r_scbond_it 1.569 r_scbond_other 1.569 r_mcbond_it 1.483 r_mcbond_other 1.482 r_angle_refined_deg 1.208 r_angle_other_deg 1.165 r_rigid_bond_restr 0.664 r_nbd_refined 0.179 r_nbd_other 0.178 r_symmetry_nbd_other 0.171 r_symmetry_xyhbond_nbd_refined 0.166 r_nbtor_refined 0.149 r_symmetry_nbd_refined 0.132 r_xyhbond_nbd_refined 0.128 r_symmetry_nbtor_other 0.073 r_symmetry_xyhbond_nbd_other 0.055 r_chiral_restr 0.052 r_gen_planes_refined 0.004 r_bond_refined_d 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 3047 Nucleic Acid Atoms Solvent Atoms 195 Heterogen Atoms
Software Software Software Name Purpose DIALS data reduction PHASER phasing REFMAC refinement Coot model building