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THE STRUCTURE OF A SENSOR DOMAIN OF A HISTIDINE KINASE (VxrA) FROM VIBRIO CHOLERAE O1 BIOVAR ELTOR STR. N16961, N239 deletion mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4R7Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 289 0.2 M LITHIUM SULFIDE,
0.1 M SODIUM,
CACODYLATE:HCL,
30% (W/V) PEG 400
Crystal Properties Matthews coefficient Solvent content 4.12 70.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.654 α = 90 b = 87.654 β = 90 c = 106.223 γ = 90
Symmetry Space Group P 41 21 2
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 PILATUS3 S 6M 2020-02-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 1.00 APS 19-ID
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 1.98 46 99.9 0.071 0.076 0.027 1 42.2 8 29036 -3 40.01
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 1.98 2.03 99.9 0.787 0.845 0.302 0.747 2.4 7.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 MOLECULAR REPLACEMENT FREE R-VALUE 4R7Q 1.98 45.42 1.35 28978 1469 98.73 0.1827 0.1813 0.1844 0.2099 0.2113 random 46.98
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 23.7266 f_angle_d 1.5237 f_chiral_restr 0.0843 f_bond_d 0.0169 f_plane_restr 0.0097
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1725 Nucleic Acid Atoms Solvent Atoms 68 Heterogen Atoms 68
Software Software Software Name Purpose SBC-Collect data collection PHENIX refinement HKL-3000 data scaling HKL-3000 data extraction HKL-3000 phasing