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High Resolution Crystal Structure of the DNA-binding Domain from the Sensor Histidine Kinase ChiS from Vibrio cholerae
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 292 Protein: 6.3 mg/ml, 0.01M Tris pH 8.3;
Screen: Classics II (G2), 0.2M Lithium sulfate, 0.1M Bis-Tris pH 5.5, 25% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.04 59.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.912 α = 90 b = 78.606 β = 90 c = 72.372 γ = 90
Symmetry Space Group C 2 2 21
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 MARMOSAIC 300 mm CCD Be 2019-12-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 1.28 30 99.7 0.076 0.076 0.083 0.032 28.3 6.9 38590 -3 14.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.28 1.3 97.3 0.757 0.757 0.854 0.386 0.637 2.3 4.6
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 (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 1.28 25.97 36482 1885 99.68 0.146 0.1443 0.1442 0.1803 0.1791 RANDOM 18.571
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] 0.12 -0.06 -0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 17.72 r_dihedral_angle_4_deg 10.412 r_dihedral_angle_3_deg 8.541 r_dihedral_angle_1_deg 2.805 r_rigid_bond_restr 1.645 r_angle_refined_deg 1.217 r_angle_other_deg 0.362 r_chiral_restr 0.055 r_gen_planes_refined 0.052 r_gen_planes_other 0.047
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 17.72 r_dihedral_angle_4_deg 10.412 r_dihedral_angle_3_deg 8.541 r_dihedral_angle_1_deg 2.805 r_rigid_bond_restr 1.645 r_angle_refined_deg 1.217 r_angle_other_deg 0.362 r_chiral_restr 0.055 r_gen_planes_refined 0.052 r_gen_planes_other 0.047 r_bond_refined_d 0.005 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 882 Nucleic Acid Atoms Solvent Atoms 228 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction HKL-3000 data scaling HKL-3000 phasing