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Crystal structure of class I SFP aldolase YihT from Salmonella enterica with SFP/ DHAP (Schiff base complex with active site Lys193)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7AG7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 30% Jeffamine M-600 v/v pH 7 and 0.1 M HEPES buffer pH 7
Crystal Properties Matthews coefficient Solvent content 2.24 45.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.774 α = 65.59 b = 82.705 β = 87.73 c = 85.203 γ = 78.21
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 XE 16M 2020-09-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
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 1.5 42.5 96.6 0.041 0.049 0.025 0.999 12.8 3.6 183409
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 1.5 1.53 94.5 0.868 1.014 0.521 0.75 3.7
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 (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 7AG7 1.5 42.48 174345 9047 96.58 0.1698 0.1686 0.1773 0.1941 0.2036 RANDOM 24.034
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] 2.06 -1.02 0.66 -1.16 0.33 -0.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.652 r_dihedral_angle_4_deg 16.972 r_dihedral_angle_3_deg 11.414 r_dihedral_angle_1_deg 5.482 r_angle_refined_deg 1.71 r_angle_other_deg 1.542 r_chiral_restr 0.091 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.652 r_dihedral_angle_4_deg 16.972 r_dihedral_angle_3_deg 11.414 r_dihedral_angle_1_deg 5.482 r_angle_refined_deg 1.71 r_angle_other_deg 1.542 r_chiral_restr 0.091 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8753 Nucleic Acid Atoms Solvent Atoms 1000 Heterogen Atoms 54
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction xia2 data reduction MOLREP phasing