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Structure of human p21 activating kinase 4 (PAK4) in complex with a consensus peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2J0I PDB entry 2J0I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 277 1.7M Ammonium sulfate, 15% PEG400, 1M Tris-HCl pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.94 58.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 145.678 α = 90 b = 145.678 β = 90 c = 39.577 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 CCD MARMOSAIC 225 mm CCD 2007-03-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.97910 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.75 50 92.5 0.057 0.057 16.3 12 43686 40410
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 1.75 1.81 94.2 0.355 5.6 4036
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 PDB entry 2J0I 1.75 32.58 40359 2020 92.47 0.185 0.182 0.1886 0.228 0.2355 RANDOM 19.143
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] 0.3 0.3 -0.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.147 r_dihedral_angle_4_deg 19.773 r_dihedral_angle_3_deg 12.871 r_dihedral_angle_1_deg 5.729 r_scangle_it 3.182 r_scbond_it 2.308 r_angle_refined_deg 1.588 r_mcangle_it 1.45 r_mcbond_it 1.102 r_angle_other_deg 1.011
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.147 r_dihedral_angle_4_deg 19.773 r_dihedral_angle_3_deg 12.871 r_dihedral_angle_1_deg 5.729 r_scangle_it 3.182 r_scbond_it 2.308 r_angle_refined_deg 1.588 r_mcangle_it 1.45 r_mcbond_it 1.102 r_angle_other_deg 1.011 r_symmetry_vdw_other 0.298 r_mcbond_other 0.294 r_nbd_refined 0.229 r_nbd_other 0.207 r_nbtor_refined 0.174 r_symmetry_hbond_refined 0.156 r_xyhbond_nbd_refined 0.135 r_symmetry_vdw_refined 0.134 r_chiral_restr 0.094 r_nbtor_other 0.088 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2379 Nucleic Acid Atoms Solvent Atoms 251 Heterogen Atoms 37
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling