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Crystal structure of death associated protein kinase in complex with ADP and Mg2+
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JKS PDB ENTRY 1JKS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 295 0.2 M ammonium chloride, 2.2 M ammonium sulfate , VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 1.91 35.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.807 α = 90 b = 62.545 β = 90 c = 88.396 γ = 90
Symmetry Space Group P 21 21 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 CCD MARMOSAIC 300 mm CCD BE LENSES 2008-10-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G APS 21-ID-G
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 1.85 30 98.1 0.066 10.6 3.8 22396 32
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) 1.85 1.92 96.3 0.469 4.15 3.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1JKS 1.85 30 21206 21206 1147 98.1 0.188 0.185 0.1845 0.244 0.24 RANDOM 25.72
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] -0.04 0.51 -0.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.681 r_dihedral_angle_4_deg 17.414 r_dihedral_angle_3_deg 16.166 r_dihedral_angle_1_deg 6.971 r_scangle_it 4.237 r_scbond_it 2.727 r_mcangle_it 1.682 r_angle_refined_deg 1.572 r_mcbond_it 1.034 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.681 r_dihedral_angle_4_deg 17.414 r_dihedral_angle_3_deg 16.166 r_dihedral_angle_1_deg 6.971 r_scangle_it 4.237 r_scbond_it 2.727 r_mcangle_it 1.682 r_angle_refined_deg 1.572 r_mcbond_it 1.034 r_nbtor_refined 0.31 r_symmetry_vdw_refined 0.229 r_nbd_refined 0.22 r_xyhbond_nbd_refined 0.159 r_symmetry_hbond_refined 0.155 r_chiral_restr 0.109 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2434 Nucleic Acid Atoms Solvent Atoms 133 Heterogen Atoms 28
Software Software Software Name Purpose BLU-MAX data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling