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Crystal structure of C-terminal catalytic domain of Plasmodium falciparum CTP:phosphocholine cytidylyltransferase with N-hydroxy-2-methylpropanimidamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4ZCS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291.15 PEG 3350 11.5%, NaF 210 mM, Glycerol 5.8%, MnCl2 15mM, 1,3 propandiol 3%
Crystal Properties Matthews coefficient Solvent content 2.41 48.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.124 α = 90 b = 67.522 β = 90 c = 117.202 γ = 90
Symmetry Space Group I 2 2 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 EIGER2 S 16M 2023-03-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.8856 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.96 46.09 96.9 0.064 0.074 0.035 0.982 11.4 4.2 22386 43.47
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.96 2.01 96.1 1.765 2.023 0.959 0.346 4.2
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.05 46.09 1.34 22386 1074 92.8 0.2125 0.2114 0.2348 0.2708 52.79
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 13.3136 f_angle_d 0.7799 f_chiral_restr 0.0527 f_bond_d 0.0077 f_plane_restr 0.0048
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1042 Nucleic Acid Atoms Solvent Atoms 43 Heterogen Atoms 11
Software Software Software Name Purpose PHENIX refinement