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Catalytic domain of histidine kinase ThkA (TM1359) in complex with ADP and Mg ion (trigonal)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other nucleotide free structure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 5% isopropanol, 2.0M ammonium sulphate, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.95 68.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.943 α = 90 b = 72.943 β = 90 c = 91.258 γ = 120
Symmetry Space Group P 32 2 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 ADSC QUANTUM 210 2006-09-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44B2 1.0 SPring-8 BL44B2
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 1.91 50 100 0.049 51.6 12.1 22342 -3 24.8
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 1.91 1.98 100 0.432 6 11.8
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 THROUGHOUT nucleotide free structure 1.91 20 22252 1133 99.99 0.186 0.185 0.1823 0.213 0.209 RANDOM 26.301
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] 0.15 0.08 0.15 -0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.697 r_dihedral_angle_3_deg 17.443 r_dihedral_angle_4_deg 15.472 r_scangle_it 9.267 r_dihedral_angle_1_deg 6.769 r_scbond_it 6.164 r_mcangle_it 4.258 r_mcbond_it 3.306 r_angle_refined_deg 1.93 r_nbtor_refined 0.339
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.697 r_dihedral_angle_3_deg 17.443 r_dihedral_angle_4_deg 15.472 r_scangle_it 9.267 r_dihedral_angle_1_deg 6.769 r_scbond_it 6.164 r_mcangle_it 4.258 r_mcbond_it 3.306 r_angle_refined_deg 1.93 r_nbtor_refined 0.339 r_nbd_refined 0.328 r_symmetry_vdw_refined 0.239 r_symmetry_hbond_refined 0.169 r_xyhbond_nbd_refined 0.115 r_chiral_restr 0.106 r_gen_planes_refined 0.013 r_bond_refined_d 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1246 Nucleic Acid Atoms Solvent Atoms 108 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing