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Crystal structure of human death associated protein kinase 3 (DAPK3) in complex with a beta-carboline ligand
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YRP PDB entry 1YRP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 277 0.1M SPG (sucrose-phosphate-glutamate buffer) pH 6.0, 30% PEG 1000, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 1.91 35.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.549 α = 90 b = 90.68 β = 100.45 c = 41.464 γ = 90
Symmetry Space Group P 1 21 1
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 2007-11-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.97926 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 1.24 50 99.5 0.079 0.079 14.7 3.7 68642 68318
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.24 1.28 100 0.707 0.707 2.04 3.6 6829
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 (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1YRP 1.24 45.36 68317 68317 3453 99.53 0.146 0.146 0.143 0.144 0.187 RANDOM 15.982
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] 0.34 -0.06 -0.42 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.863 r_sphericity_free 19.814 r_dihedral_angle_4_deg 19.334 r_dihedral_angle_3_deg 12.942 r_scangle_it 10.898 r_scbond_it 8.964 r_sphericity_bonded 8.856 r_mcangle_it 6.382 r_dihedral_angle_1_deg 5.657 r_mcbond_it 5.528
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.863 r_sphericity_free 19.814 r_dihedral_angle_4_deg 19.334 r_dihedral_angle_3_deg 12.942 r_scangle_it 10.898 r_scbond_it 8.964 r_sphericity_bonded 8.856 r_mcangle_it 6.382 r_dihedral_angle_1_deg 5.657 r_mcbond_it 5.528 r_rigid_bond_restr 4.887 r_mcbond_other 3.402 r_angle_other_deg 1.996 r_angle_refined_deg 1.703 r_nbd_refined 0.249 r_symmetry_vdw_other 0.219 r_nbd_other 0.192 r_nbtor_refined 0.184 r_symmetry_hbond_refined 0.173 r_xyhbond_nbd_refined 0.157 r_symmetry_vdw_refined 0.135 r_chiral_restr 0.128 r_nbtor_other 0.095 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 2109 Nucleic Acid Atoms Solvent Atoms 301 Heterogen Atoms 26
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection HKL-2000 data reduction