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PAK4 in complex with compound 7
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4XBU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M Bis-Tris-Propane, pH 9.0, 10% PEG 20,000
Crystal Properties Matthews coefficient Solvent content 2.22 44.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.703 α = 90 b = 62.703 β = 90 c = 149.792 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 PILATUS3 6M 2021-06-10 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 2.468 50 99.9 0.91 13.07 15.9 11390
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 2.468 2.62 0.91 1.45
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 2.468 48.124 11311 554 99.298 0.19 0.1858 0.1934 0.2627 0.2617 70.605
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] 1.806 1.806 -3.613
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.975 r_dihedral_angle_2_deg 14.941 r_dihedral_angle_6_deg 13.863 r_lrange_it 10.559 r_lrange_other 10.557 r_scangle_it 8.733 r_scangle_other 8.73 r_dihedral_angle_1_deg 7.916 r_mcangle_it 7.115 r_mcangle_other 7.112
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.975 r_dihedral_angle_2_deg 14.941 r_dihedral_angle_6_deg 13.863 r_lrange_it 10.559 r_lrange_other 10.557 r_scangle_it 8.733 r_scangle_other 8.73 r_dihedral_angle_1_deg 7.916 r_mcangle_it 7.115 r_mcangle_other 7.112 r_scbond_it 5.927 r_scbond_other 5.927 r_mcbond_it 5.027 r_mcbond_other 5.011 r_angle_refined_deg 1.712 r_angle_other_deg 0.546 r_nbd_refined 0.236 r_symmetry_nbd_other 0.21 r_nbd_other 0.209 r_symmetry_nbd_refined 0.196 r_nbtor_refined 0.185 r_xyhbond_nbd_refined 0.162 r_symmetry_xyhbond_nbd_refined 0.097 r_symmetry_nbtor_other 0.087 r_chiral_restr 0.076 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_symmetry_xyhbond_nbd_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2293 Nucleic Acid Atoms Solvent Atoms 5 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing