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Crystal structure of E. coli ThrS catalytic domain mutant L489M in complex with Obafluorin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8H98
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 .0 M ammonium sulfate, and 0.15 M sodium citrate pH 5.5. 0.02 M DL-glutamic acid monohydrate, 0.02 M DL-alanine, 0.02 M glycine, 0.02 M DL-lysine monohydrochloride, 0.02 M DL-serine, 0.061 M tris, 0.039 M bicine pH 8.5, 12.5% v/v MPD, 12.5% w/v PEG 1000, 12.5% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.33 47.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.246 α = 90 b = 84.244 β = 90 c = 102.587 γ = 90
Symmetry Space Group P 21 21 21
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 9M 2023-01-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL02U1 0.97918 SSRF BL02U1
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 3.08 84.24 91.5 0.19 0.208 0.082 0.992 9.4 6.4 15723
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 3.08 3.25 100 1.051 1.139 0.435 0.716 6.7
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3.08 36.39 1.35 15641 764 91.32 0.24 0.2379 0.2379 0.2784 0.2787
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 5.003 f_angle_d 0.467 f_chiral_restr 0.041 f_plane_restr 0.004 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6487 Nucleic Acid Atoms Solvent Atoms 12 Heterogen Atoms 54
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction MOLREP phasing