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Crystal Structure of the GGDEF domain (residues 31-260) of Diguanylate Cyclase from Vibrio cholerae serotype O1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 292 Protein: 5.6mg/ml, 0.15M Sodium chloride, 0.01M Tris pH 8.3;
Screen: PEGs II (C4), 0.2M Magnesium chloride, 0.1M MES pH 6.5, 10% (w/v) PEG4000;
Cryo: PEGs II (D3), 0.2M Magnesium chloride, 0.1M MES pH 6.5, 25% (w/v) PEG4000
Crystal Properties Matthews coefficient Solvent content 1.96 37.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.63 α = 90 b = 76.844 β = 90 c = 86.827 γ = 90
Symmetry Space Group P 21 21 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 PIXEL DECTRIS EIGER X 9M 2021-12-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 0.97895 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 30 99.4 0.173 0.173 0.048 0.999 16.3 13.5 28689 -3 24.9
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 2.03 99.7 0.313 0.794 2.5 13.6
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 2 28.79 26914 1446 99.38 0.1847 0.1817 0.1952 0.2403 0.2443 RANDOM 30.508
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] 0.31 -2.52 2.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 8.013 r_dihedral_angle_1_deg 3.161 r_dihedral_angle_2_deg 1.753 r_angle_refined_deg 1.371 r_angle_other_deg 0.447 r_chiral_restr 0.068 r_gen_planes_refined 0.02 r_gen_planes_other 0.018 r_bond_refined_d 0.005 r_bond_other_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3462 Nucleic Acid Atoms Solvent Atoms 271 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction HKL-3000 data scaling PHENIX phasing