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Crystal structure of the CCA-adding enzyme of a psychrophilic organism in complex with CTP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MIV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 protein solution at 4.5 mg/mL in50 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 5 mM CTP and reservoir solution + 18% glycerol
Crystal Properties Matthews coefficient Solvent content 3.73 66.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.38 α = 90 b = 70.38 β = 90 c = 291.49 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 PILATUS 6M 2016-09-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.979 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 1.849 50 99.8 0.069 1 22.11 12.2 63935 40.9
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 1.849 1.96 99.2 2.394 0.451 0.95 12.3
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 THROUGHOUT 1MIV 1.849 49.056 1.34 63868 3195 99.75 0.2028 0.2019 0.2062 0.2187 0.222
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 16.25 f_angle_d 0.979 f_chiral_restr 0.06 f_bond_d 0.008 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3072 Nucleic Acid Atoms Solvent Atoms 268 Heterogen Atoms 58
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHENIX phasing