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Structure of the Histidine Kinase CheA ATP-Binding domain in complex with compound ODDHK13
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 35.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.962 α = 90 b = 59.201 β = 97.162 c = 66.259 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 0.97951 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 1.8 65.74 97.3 0.045 0.054 0.029 0.999 23.1 6.5 28452
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 1.8 1.847 0.172 0.205 0.109 0.988 6.9
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.8 44.031 28436 1375 97.127 0.186 0.1845 0.1845 0.2259 0.2261 RANDOM 28.563
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] -0.401 -0.224 0.124 0.324
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 17.631 r_dihedral_angle_6_deg 16.177 r_dihedral_angle_3_deg 15.105 r_lrange_other 9.59 r_lrange_it 9.588 r_scangle_it 8.052 r_scangle_other 8.05 r_dihedral_angle_1_deg 6.213 r_scbond_it 5.41 r_scbond_other 5.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 17.631 r_dihedral_angle_6_deg 16.177 r_dihedral_angle_3_deg 15.105 r_lrange_other 9.59 r_lrange_it 9.588 r_scangle_it 8.052 r_scangle_other 8.05 r_dihedral_angle_1_deg 6.213 r_scbond_it 5.41 r_scbond_other 5.41 r_mcangle_other 3.822 r_mcangle_it 3.821 r_mcbond_it 2.888 r_mcbond_other 2.875 r_angle_refined_deg 2.071 r_angle_other_deg 0.693 r_symmetry_nbd_refined 0.38 r_nbd_other 0.304 r_nbd_refined 0.232 r_symmetry_xyhbond_nbd_refined 0.201 r_symmetry_nbd_other 0.197 r_nbtor_refined 0.182 r_dihedral_angle_other_2_deg 0.151 r_ncsr_local_group_1 0.145 r_xyhbond_nbd_refined 0.135 r_chiral_restr 0.106 r_symmetry_nbtor_other 0.084 r_bond_refined_d 0.015 r_gen_planes_refined 0.012 r_xyhbond_nbd_other 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2680 Nucleic Acid Atoms Solvent Atoms 53 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement REFMAC refinement SCALA data scaling XDS data reduction PHASER phasing