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Structure of PAK1 in complex with compound 12
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 6.6 293 0.1 M Na-malonate buffer, pH 6.6 , 0.15 M DL-malic acid, 4% propanediol, and 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.49 50.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.792 α = 90 b = 81.432 β = 106.555 c = 65.622 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 EIGER X 9M 2021-08-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.97932 NSLS-II 17-ID-1
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 2.218 29.677 96.6 0.997 9.6 5.6 30467
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 2.218 2.27 0.763 1.3
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.218 29.677 30449 1478 96.636 0.183 0.1807 0.2318 0.2456 69.541
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] -0.799 -0.451 0.676 0.332
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.154 r_dihedral_angle_6_deg 14.878 r_lrange_other 13.053 r_lrange_it 13.046 r_scangle_it 10.758 r_scangle_other 10.753 r_mcangle_other 8.351 r_mcangle_it 8.35 r_scbond_it 7.25 r_scbond_other 7.233
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.154 r_dihedral_angle_6_deg 14.878 r_lrange_other 13.053 r_lrange_it 13.046 r_scangle_it 10.758 r_scangle_other 10.753 r_mcangle_other 8.351 r_mcangle_it 8.35 r_scbond_it 7.25 r_scbond_other 7.233 r_dihedral_angle_2_deg 6.7 r_dihedral_angle_1_deg 6.699 r_mcbond_other 5.839 r_mcbond_it 5.838 r_angle_refined_deg 1.741 r_angle_other_deg 0.576 r_nbd_refined 0.219 r_symmetry_nbd_other 0.203 r_nbtor_refined 0.185 r_nbd_other 0.177 r_xyhbond_nbd_refined 0.167 r_symmetry_nbd_refined 0.089 r_symmetry_nbtor_other 0.087 r_chiral_restr 0.08 r_symmetry_xyhbond_nbd_other 0.069 r_symmetry_xyhbond_nbd_refined 0.044 r_bond_refined_d 0.008 r_chiral_restr_other 0.008 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 4383 Nucleic Acid Atoms Solvent Atoms 31 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing