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Structure of the Histidine Kinase CheA ATP-Binding domain in complex with compound ODDHK10
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 1.91 35.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.958 α = 90 b = 59.133 β = 97.041 c = 66.837 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 1.85 66.333 98.5 0.064 0.076 0.041 0.998 23.1 6.6 26744
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 1.85 1.898 0.161 0.193 0.105 0.991 6.6
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 1.85 66.333 26729 1282 98.352 0.193 0.1902 0.1898 0.2424 0.2414 19.086
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] -0.089 -0.049 -0.855 0.927
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.458 r_dihedral_angle_3_deg 15.29 r_dihedral_angle_2_deg 13.653 r_lrange_it 6.559 r_lrange_other 6.538 r_dihedral_angle_1_deg 5.861 r_scangle_it 5.124 r_scangle_other 5.123 r_scbond_it 3.4 r_scbond_other 3.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.458 r_dihedral_angle_3_deg 15.29 r_dihedral_angle_2_deg 13.653 r_lrange_it 6.559 r_lrange_other 6.538 r_dihedral_angle_1_deg 5.861 r_scangle_it 5.124 r_scangle_other 5.123 r_scbond_it 3.4 r_scbond_other 3.4 r_mcangle_other 2.582 r_mcangle_it 2.574 r_angle_refined_deg 2.167 r_mcbond_it 1.784 r_mcbond_other 1.763 r_angle_other_deg 0.71 r_dihedral_angle_other_2_deg 0.38 r_symmetry_nbd_refined 0.241 r_nbd_other 0.236 r_nbd_refined 0.234 r_symmetry_nbd_other 0.195 r_nbtor_refined 0.183 r_symmetry_xyhbond_nbd_refined 0.175 r_xyhbond_nbd_refined 0.15 r_ncsr_local_group_1 0.131 r_chiral_restr 0.108 r_symmetry_nbtor_other 0.086 r_symmetry_xyhbond_nbd_other 0.031 r_xyhbond_nbd_other 0.028 r_bond_refined_d 0.017 r_gen_planes_refined 0.013 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2683 Nucleic Acid Atoms Solvent Atoms 165 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing