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Crystal Structure of the Histidine Kinase VC2136 from Vibrio cholerae serotype O1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 292 Protein: 6.5 mg/ml, 0.15M Sodium chloride, 0.01M Tris pH 8.3;
Screen: Anions (G8), 0.37M Sodium sulfate, 0.1M MES pH 6.5.
Cryo: 2M Lithium sulfate.
Crystal Properties Matthews coefficient Solvent content 2.6 52.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.211 α = 90 b = 86.211 β = 90 c = 212.636 γ = 120
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 EIGER X 9M 2021-09-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 0.97848 APS 21-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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 2.75 30 99.9 0.106 0.106 0.034 0.995 23.9 10.7 45970 -3 68.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.75 2.8 100 0.418 0.634 1.9 10.9
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 2.75 28.22 43575 2322 99.88 0.2425 0.24022 0.2591 0.28631 0.2999 RANDOM 93.051
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] 16.29 16.29 -32.58
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 8.187 r_long_range_B_other 8.148 r_mcangle_it 3.944 r_mcangle_other 3.943 r_scangle_other 3.743 r_dihedral_angle_3_deg 2.793 r_mcbond_it 2.363 r_mcbond_other 2.362 r_scbond_it 2.316 r_scbond_other 2.209
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 8.187 r_long_range_B_other 8.148 r_mcangle_it 3.944 r_mcangle_other 3.943 r_scangle_other 3.743 r_dihedral_angle_3_deg 2.793 r_mcbond_it 2.363 r_mcbond_other 2.362 r_scbond_it 2.316 r_scbond_other 2.209 r_dihedral_angle_2_deg 1.587 r_dihedral_angle_1_deg 0.853 r_angle_refined_deg 0.845 r_angle_other_deg 0.665 r_chiral_restr 0.041 r_gen_planes_refined 0.003 r_gen_planes_other 0.003 r_bond_refined_d 0.002 r_bond_other_d 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10887 Nucleic Acid Atoms Solvent Atoms 57 Heterogen Atoms 213
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHENIX phasing