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E coli. CTP synthase in complex with dF-dCTP + ATP
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 = 158.982 α = 90 b = 108.456 β = 90 c = 128.9 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 1.6532 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 2.08 83.126 100 0.135 0.141 0.04 0.994 12.4 12.5 133846 35.3
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 2.08 2.15 100 1.862 1.944 0.556 0.684 0.8 12
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 2.08 83.126 133740 6615 99.81 0.204 0.203 0.2091 0.2215 0.2274 39.846
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] -1.406 2.187 -0.781
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.235 r_dihedral_angle_4_deg 13.454 r_dihedral_angle_3_deg 12.6 r_dihedral_angle_1_deg 5.727 r_lrange_it 4.713 r_lrange_other 4.498 r_scangle_it 2.347 r_scangle_other 2.347 r_mcangle_it 2.344 r_mcangle_other 2.344
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.235 r_dihedral_angle_4_deg 13.454 r_dihedral_angle_3_deg 12.6 r_dihedral_angle_1_deg 5.727 r_lrange_it 4.713 r_lrange_other 4.498 r_scangle_it 2.347 r_scangle_other 2.347 r_mcangle_it 2.344 r_mcangle_other 2.344 r_scbond_it 1.351 r_scbond_other 1.351 r_mcbond_it 1.342 r_mcbond_other 1.342 r_angle_refined_deg 1.178 r_angle_other_deg 1.097 r_nbd_refined 0.17 r_symmetry_nbd_other 0.159 r_nbd_other 0.156 r_nbtor_refined 0.143 r_xyhbond_nbd_refined 0.123 r_metal_ion_refined 0.111 r_symmetry_xyhbond_nbd_refined 0.1 r_symmetry_nbd_refined 0.097 r_symmetry_nbtor_other 0.068 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 8334 Nucleic Acid Atoms Solvent Atoms 659 Heterogen Atoms 126
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing