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Crystal structure of death associated protein kinase complexed with AMPPNP
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 VAPOR DIFFUSION, SITTING DROP 295 0.2 M ammonium bromide
2.2 M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 1.92 36.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.829 α = 90 b = 62.513 β = 90 c = 88.837 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 225 mm CCD Be lenses 2008-08-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
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 1.6 30 0.067 12 6.3 35350 35350 25.7
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) 1.6 1.66 0.496 4 6.2 3455
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1JKS 1.6 30 33518 1769 99.67 0.17989 0.17832 0.21015 0.2137 RANDOM 20.137
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] 0.01 0.48 -0.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.012 r_dihedral_angle_4_deg 18.004 r_dihedral_angle_3_deg 13.123 r_dihedral_angle_1_deg 5.895 r_scangle_it 3.467 r_scbond_it 2.174 r_mcangle_it 1.448 r_angle_refined_deg 1.39 r_mcbond_it 0.849 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.012 r_dihedral_angle_4_deg 18.004 r_dihedral_angle_3_deg 13.123 r_dihedral_angle_1_deg 5.895 r_scangle_it 3.467 r_scbond_it 2.174 r_mcangle_it 1.448 r_angle_refined_deg 1.39 r_mcbond_it 0.849 r_nbtor_refined 0.312 r_nbd_refined 0.209 r_symmetry_vdw_refined 0.208 r_symmetry_hbond_refined 0.153 r_xyhbond_nbd_refined 0.148 r_chiral_restr 0.087 r_bond_refined_d 0.01 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2398 Nucleic Acid Atoms Solvent Atoms 234 Heterogen Atoms 31
Software Software Software Name Purpose BLU-MAX data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling