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Structure of PAK1 in complex with compound 16
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 8 293 0.1 M Na-malonate buffer, pH 6.8 , 0.15 M DL-malic acid, 4% propanediol, and 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.43 49.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.306 α = 90 b = 80.946 β = 106.61 c = 65.883 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 2022-05-04 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 1.847 60.738 93.2 0.997 10.9 5.3 50948
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 1.847 1.879 0.603
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 1.847 60.738 50878 2562 93.023 0.19 0.1879 0.1957 0.2266 0.2283 58.183
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] 1.895 2.311 -1.047 -1.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.241 r_dihedral_angle_3_deg 14.896 r_lrange_it 10.519 r_lrange_other 10.519 r_scangle_it 8.202 r_scangle_other 8.201 r_dihedral_angle_2_deg 7.585 r_dihedral_angle_1_deg 6.381 r_mcangle_it 6.045 r_mcangle_other 6.044
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.241 r_dihedral_angle_3_deg 14.896 r_lrange_it 10.519 r_lrange_other 10.519 r_scangle_it 8.202 r_scangle_other 8.201 r_dihedral_angle_2_deg 7.585 r_dihedral_angle_1_deg 6.381 r_mcangle_it 6.045 r_mcangle_other 6.044 r_scbond_it 5.339 r_scbond_other 5.338 r_mcbond_it 4.287 r_mcbond_other 4.284 r_angle_refined_deg 1.68 r_angle_other_deg 0.56 r_symmetry_xyhbond_nbd_refined 0.438 r_nbd_refined 0.221 r_symmetry_nbd_refined 0.205 r_symmetry_nbd_other 0.198 r_nbd_other 0.196 r_nbtor_refined 0.181 r_xyhbond_nbd_refined 0.148 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.08 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 4370 Nucleic Acid Atoms Solvent Atoms 100 Heterogen Atoms 62
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing