☰ Navigation Tabs
The Crystal Structure of P21-Activated Kinases Pak4 from Biortus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CDZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 0.4 M Potassium sodium tartrate tetrahydrate
Crystal Properties Matthews coefficient Solvent content 3.43 64.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 146.274 α = 90 b = 146.274 β = 90 c = 43.68 γ = 90
Symmetry Space Group P 43 21 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 EIGER X 9M 2023-02-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.95373 CLSI 08ID-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 3.3 48.76 95.1 0.996 9.6 11 7176
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 3.3 3.56 0.809
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 3.3 46.299 7154 351 94.455 0.253 0.2494 0.2621 0.3186 0.3428 102.959
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] -8.992 -8.992 17.983
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.312 r_dihedral_angle_4_deg 13.846 r_dihedral_angle_3_deg 12.536 r_lrange_it 7.523 r_lrange_other 7.522 r_dihedral_angle_1_deg 5.008 r_mcangle_it 4.413 r_mcangle_other 4.412 r_scangle_it 4.048 r_scangle_other 4.046
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.312 r_dihedral_angle_4_deg 13.846 r_dihedral_angle_3_deg 12.536 r_lrange_it 7.523 r_lrange_other 7.522 r_dihedral_angle_1_deg 5.008 r_mcangle_it 4.413 r_mcangle_other 4.412 r_scangle_it 4.048 r_scangle_other 4.046 r_mcbond_other 2.519 r_mcbond_it 2.518 r_scbond_it 2.242 r_scbond_other 2.241 r_angle_refined_deg 1.195 r_angle_other_deg 0.982 r_nbd_refined 0.179 r_symmetry_nbd_other 0.157 r_nbtor_refined 0.143 r_xyhbond_nbd_refined 0.137 r_nbd_other 0.125 r_symmetry_nbd_refined 0.098 r_symmetry_nbtor_other 0.068 r_chiral_restr 0.035 r_symmetry_xyhbond_nbd_refined 0.035 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2328 Nucleic Acid Atoms Solvent Atoms 11 Heterogen Atoms 10
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing REFMAC refinement