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Structure of PAK1 in complex with compound 7
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 7 293 0.2 M Na-malonate, pH 7.0, 0.15 M DL-malic acid, 4% propane-diol, and 16% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.47 50.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.727 α = 90 b = 80.824 β = 107.274 c = 65.857 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 2023-07-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.9792 ALBA XALOC
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 1.84 59.9 99.4 0.055 0.063 0.029 0.998 10.1 4.4 54294
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 1.84 1.87 99.7 1.687 1.907 0.875 0.578 0.7 4.6
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.84 49.633 53968 3847 98.988 0.202 0.1968 0.2026 0.2687 0.269 RANDOM 65.625
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] -0.112 0.048 0.123 -0.034
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.907 r_dihedral_angle_6_deg 16 r_lrange_it 15.349 r_lrange_other 15.343 r_scangle_it 13.951 r_scangle_other 13.919 r_dihedral_angle_2_deg 11.776 r_mcangle_other 11.667 r_mcangle_it 11.65 r_scbond_it 11.034
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.907 r_dihedral_angle_6_deg 16 r_lrange_it 15.349 r_lrange_other 15.343 r_scangle_it 13.951 r_scangle_other 13.919 r_dihedral_angle_2_deg 11.776 r_mcangle_other 11.667 r_mcangle_it 11.65 r_scbond_it 11.034 r_scbond_other 10.96 r_mcbond_it 9.517 r_mcbond_other 9.517 r_dihedral_angle_1_deg 7.819 r_angle_refined_deg 2.54 r_angle_other_deg 0.792 r_nbd_refined 0.231 r_symmetry_nbd_other 0.219 r_symmetry_xyhbond_nbd_refined 0.219 r_nbtor_refined 0.199 r_symmetry_nbd_refined 0.187 r_nbd_other 0.18 r_xyhbond_nbd_refined 0.171 r_chiral_restr 0.124 r_symmetry_nbtor_other 0.095 r_symmetry_xyhbond_nbd_other 0.02 r_bond_refined_d 0.017 r_gen_planes_refined 0.014 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4398 Nucleic Acid Atoms Solvent Atoms 76 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing