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E coli. CTP synthase in complex with dF-dCTP
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 = 158.402 α = 90 b = 108.955 β = 90 c = 129.019 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 2019-05-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08B1-1 1 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 2.25 48.9 100 0.134 0.139 0.036 0.952 12.9 14.1 106448 38.9
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 2.25 2.33 99.9 0.82 0.853 0.233 0.798 2.06 13.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.25 48.9 106448 5316 99.905 0.191 0.1896 0.1934 0.2099 0.211 46.454
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] 0.001 -0.004 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.022 r_dihedral_angle_3_deg 13.065 r_dihedral_angle_4_deg 12.49 r_dihedral_angle_1_deg 5.719 r_lrange_it 4.589 r_lrange_other 4.51 r_mcangle_it 2.708 r_mcangle_other 2.708 r_scangle_it 2.373 r_scangle_other 2.373
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.022 r_dihedral_angle_3_deg 13.065 r_dihedral_angle_4_deg 12.49 r_dihedral_angle_1_deg 5.719 r_lrange_it 4.589 r_lrange_other 4.51 r_mcangle_it 2.708 r_mcangle_other 2.708 r_scangle_it 2.373 r_scangle_other 2.373 r_mcbond_it 1.535 r_mcbond_other 1.534 r_scbond_it 1.32 r_scbond_other 1.32 r_angle_refined_deg 1.177 r_angle_other_deg 1.081 r_nbd_other 0.186 r_symmetry_xyhbond_nbd_refined 0.167 r_nbd_refined 0.166 r_symmetry_nbd_other 0.162 r_symmetry_nbd_refined 0.155 r_nbtor_refined 0.143 r_xyhbond_nbd_refined 0.132 r_metal_ion_refined 0.112 r_symmetry_nbtor_other 0.07 r_chiral_restr 0.043 r_symmetry_xyhbond_nbd_other 0.019 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 498 Heterogen Atoms 76
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing