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Crystal structure of a psychrophilic CCA-adding enzyme in complex with CMPcPP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6QXN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 protein solution at 4.5 mg/mL in 50 mM Tris-HCl pH 7.5, 200 mM NaCl, 5 mM MgCl2;
reservoir solution: 100 mM Sodium acetate; pH 4.5
1 M di-Ammonium hydrogen phosphate
remarks : soaking 30 seconds in a drop with 10 mM CMPcPP and reservoir solution + 20% glycerol
Crystal Properties Matthews coefficient Solvent content 3.66 66.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.8 α = 90 b = 69.8 β = 90 c = 290.85 γ = 90
Symmetry Space Group P 43 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 EIGER X 16M 2020-10-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.9786 SOLEIL PROXIMA 1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 2.2 50 99.8 0.15 0.99 16.84 25.7 37711 50.85
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.34 99.3 1.616 0.786 1.98 27.1
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6QXN 2.2 46.74 1.34 37711 1886 99.84 0.2073 0.2055 0.2064 0.2424 0.2425 51.98
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 15.9797 f_angle_d 0.9303 f_chiral_restr 0.0575 f_bond_d 0.0082 f_plane_restr 0.0078
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3005 Nucleic Acid Atoms Solvent Atoms 99 Heterogen Atoms 81
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHENIX phasing