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Crystal structure of the death associated protein kinase in complex with AMPPNP 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 NaCl, 2.2 M ammonium sulfate , VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 1.9 35.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.669 α = 90 b = 62.461 β = 90 c = 88.599 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 2 30 99 0.068 9.1 6.8 18512 36.2
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) 2 2.07 87.7 0.546 3.2 6.6
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 2 30 17521 17521 941 99 0.18 0.177 0.1813 0.245 0.2435 RANDOM 30.29
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] 1.08 -0.1 -0.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.803 r_dihedral_angle_4_deg 22.44 r_dihedral_angle_3_deg 17.429 r_dihedral_angle_1_deg 6.717 r_scangle_it 4.287 r_scbond_it 2.834 r_mcangle_it 1.831 r_angle_refined_deg 1.773 r_mcbond_it 1.156 r_symmetry_hbond_refined 0.345
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.803 r_dihedral_angle_4_deg 22.44 r_dihedral_angle_3_deg 17.429 r_dihedral_angle_1_deg 6.717 r_scangle_it 4.287 r_scbond_it 2.834 r_mcangle_it 1.831 r_angle_refined_deg 1.773 r_mcbond_it 1.156 r_symmetry_hbond_refined 0.345 r_nbtor_refined 0.311 r_symmetry_vdw_refined 0.258 r_nbd_refined 0.229 r_xyhbond_nbd_refined 0.155 r_chiral_restr 0.134 r_bond_refined_d 0.018 r_gen_planes_refined 0.007 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 2453 Nucleic Acid Atoms Solvent Atoms 99 Heterogen Atoms 37
Software Software Software Name Purpose BLU-MAX data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling