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Structure of PAK1 in complex with compound 24
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5DEW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 100 mM malonate pH 6.6, 150 mM malic acid, 19% PEG 3350, 4% 1,2-propanediol
Crystal Properties Matthews coefficient Solvent content 2.26 45.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.267 α = 90 b = 80.951 β = 108.797 c = 65.634 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 PILATUS 6M 2022-04-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.97918 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.898 54.213 99.8 0.997 9.8 5.51 44800
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.898 1.93 0.564 1.7
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 1.898 54.213 44799 2331 99.791 0.186 0.1839 0.1901 0.2299 0.2342 47.126
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] 0.037 0.106 0.051 -0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.271 r_dihedral_angle_3_deg 13.414 r_dihedral_angle_2_deg 9.679 r_lrange_other 7.774 r_lrange_it 7.768 r_dihedral_angle_1_deg 6.589 r_scangle_it 6.297 r_scangle_other 6.296 r_mcangle_it 4.333 r_mcangle_other 4.332
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.271 r_dihedral_angle_3_deg 13.414 r_dihedral_angle_2_deg 9.679 r_lrange_other 7.774 r_lrange_it 7.768 r_dihedral_angle_1_deg 6.589 r_scangle_it 6.297 r_scangle_other 6.296 r_mcangle_it 4.333 r_mcangle_other 4.332 r_scbond_it 4.231 r_scbond_other 4.23 r_mcbond_it 3.117 r_mcbond_other 3.113 r_angle_refined_deg 1.716 r_angle_other_deg 0.556 r_nbd_other 0.228 r_nbd_refined 0.209 r_symmetry_nbd_other 0.191 r_xyhbond_nbd_refined 0.181 r_symmetry_nbd_refined 0.18 r_symmetry_xyhbond_nbd_refined 0.179 r_nbtor_refined 0.176 r_chiral_restr 0.087 r_symmetry_nbtor_other 0.083 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4339 Nucleic Acid Atoms Solvent Atoms 179 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing