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Structure of the Histidine Kinase CheA ATP-Binding domain in complex with compound ODDHK8
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1I58
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 294.15 PEG 8000 30% Ammonium acetate 0.6 M Sodium acetate 0.065 M ph 4.5
Crystal Properties Matthews coefficient Solvent content 1.89 35.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.978 α = 90 b = 59.021 β = 97.318 c = 66.526 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 PIXEL DECTRIS PILATUS 6M 2019-04-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.979510 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2 65.98 98.5 0.053 0.063 0.033 0.999 20.3 6.6 21093
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.052 0.187 0.222 0.118 0.987 6.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2 44.029 21078 1010 98.321 0.188 0.1848 0.1842 0.2435 0.2421 28.68
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] -1.093 -0.299 -0.791 1.898
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.14 r_dihedral_angle_6_deg 16.355 r_dihedral_angle_2_deg 11.504 r_lrange_other 9.03 r_lrange_it 9.027 r_scangle_it 7.935 r_scangle_other 7.933 r_dihedral_angle_1_deg 6.421 r_scbond_it 5.249 r_scbond_other 5.249
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.14 r_dihedral_angle_6_deg 16.355 r_dihedral_angle_2_deg 11.504 r_lrange_other 9.03 r_lrange_it 9.027 r_scangle_it 7.935 r_scangle_other 7.933 r_dihedral_angle_1_deg 6.421 r_scbond_it 5.249 r_scbond_other 5.249 r_mcangle_it 4.566 r_mcangle_other 4.564 r_mcbond_it 3.468 r_mcbond_other 3.461 r_angle_refined_deg 2.043 r_angle_other_deg 0.66 r_symmetry_nbd_refined 0.356 r_nbd_other 0.318 r_nbd_refined 0.24 r_symmetry_nbd_other 0.193 r_nbtor_refined 0.179 r_xyhbond_nbd_refined 0.157 r_ncsr_local_group_1 0.142 r_symmetry_xyhbond_nbd_refined 0.122 r_chiral_restr 0.094 r_symmetry_nbtor_other 0.085 r_dihedral_angle_other_2_deg 0.041 r_bond_refined_d 0.014 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2668 Nucleic Acid Atoms Solvent Atoms 75 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing