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Diguanylate cyclase Q15Z91 complex with c-di-GMP and GTP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BRE We used 3BRE REC domain and effector domain as two ensembles
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 277 Q15Z91 was pre-incubated with 5 mM Magnesium chloride, 200 uM Zinc chloride, and 3 mM GTP with crystallization solution (8% v/v tacsimate, pH 7.0, 20% w/v polyethylene glycol 3,350)
Crystal Properties Matthews coefficient Solvent content 2.91 57.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.865 α = 90 b = 116.493 β = 90 c = 167.289 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 CCD MARMOSAIC 300 mm CCD 2015-06-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 0.98178 APS 21-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.94 47.8 97.9 0.103 13.5 6.1 116921 29.99
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9444 1.993 0.54 2.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.94 47.8 1.34 116921 1992 97.9 0.2015 0.2008 0.2025 0.2388 0.2416 47.88
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 10.0282 f_angle_d 1.3535 f_chiral_restr 0.061 f_bond_d 0.012 f_plane_restr 0.0069
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9297 Nucleic Acid Atoms Solvent Atoms 521 Heterogen Atoms 531
Software Software Software Name Purpose HKL-2000 data reduction HKL-2000 data scaling PHASER phasing Coot model building PHENIX refinement