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Structure of S. pombe CC-Adding Enzyme in complex with CTP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9NS2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 Protein solution (6.5 mg/ml in 20 mM Tris pH 7.5, 50 mM NaCl) was mixed 1.5:1 with well solution (7% w/v PEG 8000, 100 mM HEPES pH 7.5, 7% v/v ethylene glycol). Cyro condition was well solution with 20% ethylene glycol, 5mM CTP, and 5mM magnesium chloride added
Crystal Properties Matthews coefficient Solvent content 2.89 57.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.192 α = 90 b = 67.725 β = 90 c = 162.973 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 16M 2018-02-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0332 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.05 34.91 98.6 0.998 12.12 4.88 41388 54.02
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.17 99.3 0.636 1.21 5.04
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 FOURIER SYNTHESIS FREE R-VALUE 2.05 34.91 1.34 77794 3728 98 0.1948 0.193 0.1945 0.2295 0.2285 69.63
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 19.2417 f_angle_d 0.8916 f_chiral_restr 0.0523 f_bond_d 0.0073 f_plane_restr 0.0067
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3693 Nucleic Acid Atoms Solvent Atoms 165 Heterogen Atoms 70
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing