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E coli. CTP synthase in complex with dF-dCTP + ADP
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 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 = 158.014 α = 90 b = 109.426 β = 90 c = 129.023 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 CCD RAYONIX MX-300 2021-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08B1-1 1.6534 CLSI 08B1-1
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 2.05 83.5 100 0.098 0.102 0.029 0.997 12.7 12.2 140206 38.6
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 2.05 2.12 100 1.567 1.641 0.749 0.749 0.8 10.2
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 2.05 83.5 140066 6950 99.766 0.198 0.1973 0.2035 0.2159 0.2209 48.089
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] -0.504 0.396 0.107
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.989 r_dihedral_angle_4_deg 13.855 r_dihedral_angle_3_deg 13.548 r_dihedral_angle_1_deg 6.082 r_lrange_it 5.299 r_lrange_other 5.178 r_mcangle_it 2.134 r_mcangle_other 2.134 r_scangle_it 2.048 r_scangle_other 2.048
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.989 r_dihedral_angle_4_deg 13.855 r_dihedral_angle_3_deg 13.548 r_dihedral_angle_1_deg 6.082 r_lrange_it 5.299 r_lrange_other 5.178 r_mcangle_it 2.134 r_mcangle_other 2.134 r_scangle_it 2.048 r_scangle_other 2.048 r_angle_refined_deg 1.239 r_mcbond_it 1.226 r_mcbond_other 1.226 r_scbond_it 1.176 r_scbond_other 1.176 r_angle_other_deg 1.155 r_nbd_refined 0.177 r_symmetry_nbd_other 0.165 r_symmetry_nbd_refined 0.158 r_nbd_other 0.148 r_nbtor_refined 0.147 r_xyhbond_nbd_refined 0.139 r_symmetry_xyhbond_nbd_other 0.126 r_symmetry_xyhbond_nbd_refined 0.122 r_symmetry_nbtor_other 0.069 r_metal_ion_refined 0.068 r_chiral_restr 0.053 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8334 Nucleic Acid Atoms Solvent Atoms 548 Heterogen Atoms 116
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing