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Crystal structure of E. coli ThrS catalytic domain mutant G463S
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8H99
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 0.02 M sodium formate, 0.02 M ammonium acetate, 0.02 M sodium citrate tribasic, 0.02 M potassium sodium tartrate tetrahydrate, 0.02 M sodium oxamate, 0.045 M imidazole, 0.055 M MES monohydrate acid pH 6.5, 20% v/v PEG 500 MME, 10% w/v PEG 20000
Crystal Properties Matthews coefficient Solvent content 2.87 57.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.964 α = 90 b = 107.408 β = 90 c = 112.793 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 EIGER X 16M 2023-01-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL10U2 0.97918 SSRF BL10U2
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 1.96 77.78 97.2 0.089 0.096 0.035 0.998 12.9 7.3 77887
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 1.96 2.06 99.9 0.922 0.99 0.356 0.821 7.5
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 1.96 42.18 1.36 77734 3843 97.07 0.2135 0.2122 0.2126 0.2369 0.2369
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 4.664 f_angle_d 0.481 f_chiral_restr 0.042 f_plane_restr 0.004 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6529 Nucleic Acid Atoms Solvent Atoms 574 Heterogen Atoms 2
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction MOLREP phasing