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High-resolution crystallographic analysis of the autoinhibited conformation of a human death-associated protein kinase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2A27
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 295 PEG4000, glycerol, DTT, Tris, lithium sulfate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.2 43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.3 α = 92.16 b = 60.65 β = 103.45 c = 98.71 γ = 94.25
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 MARRESEARCH 2004-07-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7A 0.9206 EMBL/DESY, HAMBURG BW7A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.47 40 94.8 0.049 11.1 2.5 200389 200389 -3 -3 27
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.47 1.52 93.4 0.424 1.9 1.9 18844
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2A27 1.47 20 -3 200335 200335 2003 94.82 0.15016 0.15016 0.14959 0.1529 0.20688 0.2118 RANDOM 23.625
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] 0.57 -0.24 1.01 0.36 -0.2 -0.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.947 r_dihedral_angle_4_deg 17.967 r_sphericity_free 14.73 r_dihedral_angle_3_deg 13.953 r_scangle_it 9.187 r_scbond_it 6.908 r_dihedral_angle_1_deg 5.934 r_sphericity_bonded 5.875 r_mcangle_it 5.22 r_mcbond_it 4.102
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.947 r_dihedral_angle_4_deg 17.967 r_sphericity_free 14.73 r_dihedral_angle_3_deg 13.953 r_scangle_it 9.187 r_scbond_it 6.908 r_dihedral_angle_1_deg 5.934 r_sphericity_bonded 5.875 r_mcangle_it 5.22 r_mcbond_it 4.102 r_rigid_bond_restr 3.578 r_mcbond_other 2.061 r_angle_refined_deg 1.599 r_angle_other_deg 0.873 r_nbd_refined 0.233 r_metal_ion_refined 0.215 r_symmetry_vdw_other 0.203 r_nbd_other 0.188 r_symmetry_hbond_refined 0.185 r_nbtor_refined 0.178 r_xyhbond_nbd_refined 0.176 r_chiral_restr 0.107 r_symmetry_vdw_refined 0.103 r_nbtor_other 0.085 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9884 Nucleic Acid Atoms Solvent Atoms 1371 Heterogen Atoms 61
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing