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The MgF3(H2O) transition state analog complex of E. coli YihX
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2B0C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 20 mg/mL YihX in Tris-HCl 25 mM pH 7.5, NaCl 150 mM, MgCl2 20 mM, NaF 30 mM was mixed 1:1 ratio with precipitant containing MES 55.5 mM, imidazole 44.5 mM pH 6.5, 20% PEG500, 30 mM MgCl2, 30 mM CaCl2, 20% glycerol, 10% PEG4000. The crystals are further soaked with the precipitant supplemented with 50 mM MgCl2 and 100 mM NH4F
Crystal Properties Matthews coefficient Solvent content 4.43 71.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.259 α = 90 b = 79.325 β = 108.52 c = 80.297 γ = 90
Symmetry Space Group P 1 21 1
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 XE 16M 2022-04-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9762 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.2 58.97 100 0.992 5.8 6.9 40811
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.27 0.664 1
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.2 59.04 38765 2023 99.92 0.21376 0.21152 0.2225 0.25711 0.2657 RANDOM 38.806
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] -0.33 -0.56 -3.87 3.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.471 r_dihedral_angle_2_deg 8.552 r_long_range_B_refined 7.69 r_long_range_B_other 7.689 r_dihedral_angle_1_deg 7.156 r_scangle_other 5.431 r_mcangle_it 4.802 r_mcangle_other 4.801 r_scbond_it 3.721 r_scbond_other 3.721
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.471 r_dihedral_angle_2_deg 8.552 r_long_range_B_refined 7.69 r_long_range_B_other 7.689 r_dihedral_angle_1_deg 7.156 r_scangle_other 5.431 r_mcangle_it 4.802 r_mcangle_other 4.801 r_scbond_it 3.721 r_scbond_other 3.721 r_mcbond_it 3.183 r_mcbond_other 3.182 r_angle_refined_deg 1.481 r_angle_other_deg 0.489 r_chiral_restr 0.065 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3196 Nucleic Acid Atoms Solvent Atoms 231 Heterogen Atoms 111
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling MOLREP phasing