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Crystal structure of a glycine-rich loop mutant of the death associated protein kinase catalytic domain
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, HANGING DROP 7.5 295 100 mM Tris pH 7.5, 0.8 M Ammonium Sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 1.92 36.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.208 α = 90 b = 62.441 β = 90 c = 88.576 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 Mirror 2006-07-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 1.0000 APS 22-BM
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 1.7 50 95.6 0.074 4.8 28268 28268 -3
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 1.7 1.75 92.7 0.526 2.3 3.4 2682
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 1.7 25.52 26817 26817 1431 95.83 0.17534 0.17292 0.1729 0.21999 0.219 RANDOM 20.727
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] 0.28 -0.13 -0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.251 r_dihedral_angle_4_deg 18.453 r_dihedral_angle_3_deg 11.168 r_scangle_it 4.615 r_dihedral_angle_1_deg 4.48 r_scbond_it 2.977 r_mcangle_it 1.798 r_angle_refined_deg 1.53 r_mcbond_it 1.152 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.251 r_dihedral_angle_4_deg 18.453 r_dihedral_angle_3_deg 11.168 r_scangle_it 4.615 r_dihedral_angle_1_deg 4.48 r_scbond_it 2.977 r_mcangle_it 1.798 r_angle_refined_deg 1.53 r_mcbond_it 1.152 r_nbtor_refined 0.31 r_nbd_refined 0.231 r_symmetry_vdw_refined 0.218 r_symmetry_hbond_refined 0.203 r_xyhbond_nbd_refined 0.175 r_chiral_restr 0.11 r_bond_refined_d 0.016 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2229 Nucleic Acid Atoms Solvent Atoms 221 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement SERGUI data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing