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Crystal structure of phosphorylated 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 6.5, 1.1 M ammonium tartrate, 0.2 M guanidine hydrochloride
Crystal Properties Matthews coefficient Solvent content 3.46 64.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.975 α = 90 b = 102.975 β = 90 c = 157.686 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 2021-04-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.54187
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 1.85 34 98.9 0.999 24 17.2 42174
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.89 0.798 0.843 2.2
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 1.85 29.552 42167 2157 98.468 0.189 0.1875 0.1973 0.2088 0.2148 32.657
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] 0.096 0.048 0.096 -0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.231 r_dihedral_angle_3_deg 12.983 r_lrange_it 9.034 r_lrange_other 8.853 r_scangle_other 7.134 r_scangle_it 7.13 r_dihedral_angle_1_deg 5.839 r_dihedral_angle_2_deg 5.141 r_scbond_it 4.715 r_scbond_other 4.713
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.231 r_dihedral_angle_3_deg 12.983 r_lrange_it 9.034 r_lrange_other 8.853 r_scangle_other 7.134 r_scangle_it 7.13 r_dihedral_angle_1_deg 5.839 r_dihedral_angle_2_deg 5.141 r_scbond_it 4.715 r_scbond_other 4.713 r_mcangle_it 4.352 r_mcangle_other 4.351 r_mcbond_it 3.294 r_mcbond_other 3.29 r_angle_refined_deg 1.643 r_angle_other_deg 0.571 r_symmetry_nbd_refined 0.218 r_nbd_refined 0.214 r_dihedral_angle_other_2_deg 0.21 r_symmetry_nbd_other 0.193 r_nbtor_refined 0.171 r_xyhbond_nbd_refined 0.169 r_symmetry_xyhbond_nbd_refined 0.148 r_nbd_other 0.114 r_chiral_restr 0.089 r_symmetry_nbtor_other 0.078 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2356 Nucleic Acid Atoms Solvent Atoms 322 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing