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Catalytic domain of histidine kinase ThkA (TM1359) (nucleotide free form 1: ammomium phosphate, monoclinic)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3A0W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 0.4M ammonium phosphate, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.89 34.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.593 α = 90 b = 46.128 β = 112.26 c = 38.65 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 ADSC QUANTUM 210 2007-07-05 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 1.89 50 94.6 0.049 15.4 3 10091 -3 22.1
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) 1.9 1.97 94.6 0.284 3.6 2.6
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 3A0W 1.89 37.56 10072 485 93.89 0.218 0.214 0.2361 0.287 0.2919 RANDOM 27.853
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] 1.72 0.48 0.38 -1.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.82 r_dihedral_angle_4_deg 18.629 r_dihedral_angle_3_deg 16.569 r_dihedral_angle_1_deg 5.922 r_scangle_it 3.627 r_scbond_it 2.321 r_angle_refined_deg 1.58 r_mcangle_it 1.537 r_mcbond_it 1.119 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.82 r_dihedral_angle_4_deg 18.629 r_dihedral_angle_3_deg 16.569 r_dihedral_angle_1_deg 5.922 r_scangle_it 3.627 r_scbond_it 2.321 r_angle_refined_deg 1.58 r_mcangle_it 1.537 r_mcbond_it 1.119 r_nbtor_refined 0.31 r_nbd_refined 0.211 r_xyhbond_nbd_refined 0.194 r_symmetry_vdw_refined 0.191 r_symmetry_hbond_refined 0.169 r_chiral_restr 0.11 r_bond_refined_d 0.011 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1254 Nucleic Acid Atoms Solvent Atoms 96 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing