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Crystal structure of kinase domain of Human 5'-AMP-activated protein kinase alpha-2 subunit mutant (T172D)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2H6D PDB ENTRY 2H6D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.9 293 0.1M Tris-HCl pH8.9, 16% PEG4000, 15% isopropanol, 0.1M Ammonium sulfate, Protein solution: 5mM AMPPNP, 5mM Magnesium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.11 41.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.187 α = 90 b = 67.336 β = 91.26 c = 50.651 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 RIGAKU JUPITER 210 rhodium coated mirror 2006-09-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B2 1.000 SPring-8 BL26B2
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 3 25 94.3 0.106 11.5 3 4913 48.3
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 3 3.05 51.6 0.251 3.2 1.7 126
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2H6D 3.02 25 4422 484 93.31 0.235 0.227 0.2276 0.308 0.2185 RANDOM 21.753
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] 0.99 0.51 0.15 -1.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.402 r_dihedral_angle_3_deg 15.713 r_dihedral_angle_4_deg 13.511 r_dihedral_angle_1_deg 4.405 r_angle_refined_deg 0.873 r_scangle_it 0.444 r_mcangle_it 0.315 r_nbtor_refined 0.295 r_scbond_it 0.26 r_mcbond_it 0.177
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.402 r_dihedral_angle_3_deg 15.713 r_dihedral_angle_4_deg 13.511 r_dihedral_angle_1_deg 4.405 r_angle_refined_deg 0.873 r_scangle_it 0.444 r_mcangle_it 0.315 r_nbtor_refined 0.295 r_scbond_it 0.26 r_mcbond_it 0.177 r_symmetry_vdw_refined 0.168 r_nbd_refined 0.166 r_xyhbond_nbd_refined 0.092 r_symmetry_hbond_refined 0.086 r_chiral_restr 0.055 r_bond_refined_d 0.006 r_gen_planes_refined 0.002 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 2063 Nucleic Acid Atoms Solvent Atoms 10 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement BSS data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing