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Crystal structure of SFP aldolase YihT from Salmonella enterica in complex with sulfate bound at the active site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TO3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 25% PEG 3350, 0.2 M Na2SO4, 0.1M BisTris propane pH7.5
Crystal Properties Matthews coefficient Solvent content 3.44 64.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.207 α = 107.42 b = 107.233 β = 95.93 c = 126.855 γ = 110.55
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 2019-09-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97625 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 1.8 53.71 97.5 0.043 0.055 0.034 0.998 9.2 2.2 352557
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 1.8 1.83 96.1 0.324 0.425 0.272 0.841 2.1
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 1TO3 1.8 53.01 335012 17503 97.47 0.1937 0.193 0.2004 0.2073 0.2155 RANDOM 26.46
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] -0.94 -0.32 -0.46 1.09 -0.11 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.169 r_dihedral_angle_4_deg 17.417 r_dihedral_angle_3_deg 11.847 r_dihedral_angle_1_deg 5.371 r_angle_other_deg 1.466 r_angle_refined_deg 1.457 r_chiral_restr 0.078 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.169 r_dihedral_angle_4_deg 17.417 r_dihedral_angle_3_deg 11.847 r_dihedral_angle_1_deg 5.371 r_angle_other_deg 1.466 r_angle_refined_deg 1.457 r_chiral_restr 0.078 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 25659 Nucleic Acid Atoms Solvent Atoms 1870 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction xia2 data reduction MOLREP phasing