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E coli. CTP synthase in complex with dF-dCTP (potassium malonate + 5 mM MgCl2)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5TKV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 277 0.1 M TRIS-Cl pH 8.0 (room temperature), 5 mM magnesium chloride, 1.15 - 1.4 M ammonium sulfate, 15 mg/mL CTPS.
Crystal Properties Matthews coefficient Solvent content 4.54 72.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 165.796 α = 90 b = 103.967 β = 90 c = 131.888 γ = 90
Symmetry Space Group P 21 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 EIGER2 X 16M 2022-01-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE 7B2 1.3777 CHESS 7B2
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 2.28 81.7 99.9 0.141 0.147 0.041 0.994 9.7 12.4 103987 42.2
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 2.28 2.36 98.8 1.15 1.243 0.458 0.629 0.8 7.11
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5TKV 2.281 81.7 103987 5239 99.721 0.195 0.1934 0.199 0.2185 0.2244 45.715
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] -1.888 3.558 -1.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.284 r_dihedral_angle_3_deg 12.679 r_dihedral_angle_4_deg 12.384 r_dihedral_angle_1_deg 5.736 r_lrange_it 5.168 r_lrange_other 5.101 r_scangle_it 3.091 r_scangle_other 3.091 r_mcangle_it 2.905 r_mcangle_other 2.904
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.284 r_dihedral_angle_3_deg 12.679 r_dihedral_angle_4_deg 12.384 r_dihedral_angle_1_deg 5.736 r_lrange_it 5.168 r_lrange_other 5.101 r_scangle_it 3.091 r_scangle_other 3.091 r_mcangle_it 2.905 r_mcangle_other 2.904 r_scbond_it 1.744 r_scbond_other 1.743 r_mcbond_it 1.687 r_mcbond_other 1.687 r_angle_refined_deg 1.189 r_angle_other_deg 1.09 r_nbd_refined 0.167 r_symmetry_nbd_other 0.159 r_nbtor_refined 0.141 r_symmetry_nbd_refined 0.14 r_nbd_other 0.132 r_xyhbond_nbd_refined 0.119 r_symmetry_xyhbond_nbd_refined 0.09 r_symmetry_nbtor_other 0.068 r_symmetry_xyhbond_nbd_other 0.055 r_chiral_restr 0.045 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8326 Nucleic Acid Atoms Solvent Atoms 476 Heterogen Atoms 88
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling MOLREP phasing