☰ Navigation Tabs
Crystal structure of AMP-PNP-bound PAK2 kinase domain containing D368N 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 HEPES pH 7.0, 25% PEG 6000, 0.2 M MgCl2
Crystal Properties Matthews coefficient Solvent content 2.35 47.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.938 α = 90 b = 67.053 β = 91.055 c = 183.319 γ = 90
Symmetry Space Group C 1 2 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 PILATUS3 R 200K-A 2022-07-04 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) 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 50 95.3 0.084 0.997 19.8 7.6 86810
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 2 2.07 0.769 0.543 1.9
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 22.699 86802 4305 90.503 0.196 0.1948 0.1988 0.2284 0.2304 48.7
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] -7.856 1.873 -1.019 8.876
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.527 r_dihedral_angle_3_deg 14.403 r_lrange_other 11.371 r_lrange_it 11.363 r_scangle_it 7.703 r_scangle_other 7.702 r_dihedral_angle_1_deg 6.926 r_mcangle_it 6.922 r_mcangle_other 6.922 r_dihedral_angle_2_deg 6.118
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.527 r_dihedral_angle_3_deg 14.403 r_lrange_other 11.371 r_lrange_it 11.363 r_scangle_it 7.703 r_scangle_other 7.702 r_dihedral_angle_1_deg 6.926 r_mcangle_it 6.922 r_mcangle_other 6.922 r_dihedral_angle_2_deg 6.118 r_scbond_it 5.328 r_scbond_other 5.322 r_mcbond_it 4.916 r_mcbond_other 4.916 r_angle_refined_deg 1.575 r_angle_other_deg 0.539 r_nbd_refined 0.195 r_symmetry_nbd_other 0.193 r_nbd_other 0.191 r_nbtor_refined 0.176 r_symmetry_nbd_refined 0.147 r_symmetry_xyhbond_nbd_refined 0.132 r_xyhbond_nbd_refined 0.121 r_chiral_restr 0.082 r_symmetry_nbtor_other 0.078 r_dihedral_angle_other_2_deg 0.02 r_chiral_restr_other 0.016 r_bond_refined_d 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 9317 Nucleic Acid Atoms Solvent Atoms 286 Heterogen Atoms 70
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing