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The Crystal Structure of PAK1 kinase domain from Biortus.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YHV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1M SPG pH6.0, 25% PEG 1500
Crystal Properties Matthews coefficient Solvent content 2.45 49.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.823 α = 90 b = 103.262 β = 90 c = 122.182 γ = 90
Symmetry Space Group C 2 2 21
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 6M 2021-08-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 1.1806 CLSI 08ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.8 47.56 100 0.055 18.3 6.4 30827
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.84 0.77
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 1.8 46.36 30795 1533 99.958 0.171 0.1684 0.1791 0.2161 0.2263 33.321
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] 3.023 -1.358 -1.665
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.534 r_dihedral_angle_3_deg 14.66 r_dihedral_angle_2_deg 9.583 r_lrange_it 8.089 r_lrange_other 7.976 r_dihedral_angle_1_deg 6.48 r_scangle_it 6.389 r_scangle_other 6.388 r_mcangle_it 4.292 r_mcangle_other 4.291
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.534 r_dihedral_angle_3_deg 14.66 r_dihedral_angle_2_deg 9.583 r_lrange_it 8.089 r_lrange_other 7.976 r_dihedral_angle_1_deg 6.48 r_scangle_it 6.389 r_scangle_other 6.388 r_mcangle_it 4.292 r_mcangle_other 4.291 r_scbond_it 4.162 r_scbond_other 4.159 r_mcbond_it 3.17 r_mcbond_other 3.166 r_angle_refined_deg 1.458 r_angle_other_deg 0.496 r_symmetry_xyhbond_nbd_refined 0.242 r_nbd_refined 0.221 r_nbd_other 0.207 r_xyhbond_nbd_refined 0.198 r_symmetry_nbd_other 0.188 r_nbtor_refined 0.172 r_symmetry_nbd_refined 0.163 r_symmetry_nbtor_other 0.079 r_chiral_restr 0.075 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2298 Nucleic Acid Atoms Solvent Atoms 273 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing