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PAK4 kinase domain in complex with FRAX486
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4FIJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 0.1 M Tris-HCl (pH 7.5) and 1.5 - 2.0 M Na acetate
Crystal Properties Matthews coefficient Solvent content 2.52 51.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.955 α = 90 b = 62.955 β = 90 c = 183.509 γ = 90
Symmetry Space Group P 41 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 CCD ADSC QUANTUM 315 2015-11-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.97919 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) 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 2.5 50 99.9 0.021 23.1 20.1 13760
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.59 100 0.835 1.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4FIJ 2.5 50 12529 704 97.8 0.231 0.22839 0.2294 0.27564 0.2764 RANDOM 115.572
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] 3.21 3.21 -6.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.657 r_dihedral_angle_4_deg 19.275 r_long_range_B_refined 18.984 r_long_range_B_other 18.98 r_dihedral_angle_3_deg 15.884 r_scangle_other 14.492 r_mcangle_it 13.355 r_mcangle_other 13.351 r_scbond_it 9.791 r_scbond_other 9.787
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.657 r_dihedral_angle_4_deg 19.275 r_long_range_B_refined 18.984 r_long_range_B_other 18.98 r_dihedral_angle_3_deg 15.884 r_scangle_other 14.492 r_mcangle_it 13.355 r_mcangle_other 13.351 r_scbond_it 9.791 r_scbond_other 9.787 r_mcbond_it 9.372 r_mcbond_other 9.369 r_dihedral_angle_1_deg 7.061 r_angle_refined_deg 1.691 r_angle_other_deg 1.027 r_chiral_restr 0.09 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2295 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing