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Structure of PAK4 in complex with compound 18
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2J0I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M HEPES pH 7.5, 4% (v/v) PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.75 55.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.642 α = 90 b = 62.642 β = 90 c = 184.886 γ = 90
Symmetry Space Group P 41 21 2
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 2021-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.97926 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 2.449 44.334 99.4 0.999 13.1 9.7 14318
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 2.449 2.46 0.515 1
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 2.449 44.334 14291 720 99.714 0.205 0.201 0.2058 0.2872 0.2873 70.203
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] 0.253 0.253 -0.506
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.359 r_dihedral_angle_6_deg 15.113 r_lrange_other 10.54 r_lrange_it 10.539 r_scangle_it 8.919 r_scangle_other 8.916 r_dihedral_angle_1_deg 7.971 r_mcangle_it 7.768 r_mcangle_other 7.766 r_dihedral_angle_2_deg 7.036
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.359 r_dihedral_angle_6_deg 15.113 r_lrange_other 10.54 r_lrange_it 10.539 r_scangle_it 8.919 r_scangle_other 8.916 r_dihedral_angle_1_deg 7.971 r_mcangle_it 7.768 r_mcangle_other 7.766 r_dihedral_angle_2_deg 7.036 r_scbond_it 6.69 r_scbond_other 6.688 r_mcbond_it 6.031 r_mcbond_other 6.022 r_angle_refined_deg 2.514 r_angle_other_deg 0.795 r_nbd_other 0.252 r_nbd_refined 0.238 r_symmetry_nbd_other 0.217 r_nbtor_refined 0.19 r_xyhbond_nbd_refined 0.167 r_chiral_restr 0.116 r_symmetry_nbtor_other 0.092 r_symmetry_xyhbond_nbd_other 0.086 r_symmetry_nbd_refined 0.076 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2289 Nucleic Acid Atoms Solvent Atoms 42 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing