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Crystal structure of nucleotide-bound PAK2 kinase domain containing K278R mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3Q52
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 0.1 M MES, pH 6.3, 1.15 M ammonium tartrate, 0.2 M guanidine hydrochloride
Crystal Properties Matthews coefficient Solvent content 3.46 64.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.911 α = 90 b = 102.911 β = 90 c = 157.65 γ = 120
Symmetry Space Group P 63 2 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 R 200K-A 2022-06-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.54
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 1.9 50 99.8 0.147 0.152 0.037 0.999 20.4 15.8 39574
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.97 100 1.22 0.42 0.596 2 9.4
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 1.9 21.441 39515 1930 99.722 0.189 0.1881 0.1961 0.215 0.224 29.264
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] 0.022 0.011 0.022 -0.071
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.837 r_dihedral_angle_3_deg 12.751 r_lrange_it 8.894 r_lrange_other 8.795 r_dihedral_angle_1_deg 5.788 r_scangle_other 5.69 r_scangle_it 5.688 r_dihedral_angle_2_deg 5.519 r_scbond_it 3.524 r_scbond_other 3.522
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.837 r_dihedral_angle_3_deg 12.751 r_lrange_it 8.894 r_lrange_other 8.795 r_dihedral_angle_1_deg 5.788 r_scangle_other 5.69 r_scangle_it 5.688 r_dihedral_angle_2_deg 5.519 r_scbond_it 3.524 r_scbond_other 3.522 r_mcangle_it 3.469 r_mcangle_other 3.468 r_mcbond_it 2.292 r_mcbond_other 2.271 r_angle_refined_deg 1.38 r_angle_other_deg 0.492 r_symmetry_xyhbond_nbd_refined 0.219 r_nbd_refined 0.208 r_symmetry_nbd_other 0.186 r_xyhbond_nbd_refined 0.175 r_nbtor_refined 0.172 r_symmetry_nbd_refined 0.156 r_nbd_other 0.13 r_chiral_restr 0.075 r_symmetry_nbtor_other 0.075 r_chiral_restr_other 0.072 r_dihedral_angle_other_2_deg 0.01 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2352 Nucleic Acid Atoms Solvent Atoms 281 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing