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Crystal structure of metal-dependent class II sulfofructose phosphate aldolase from Yersinia aldovae in complex with sulfofructose phosphate (YaSqiA-Zn-SFP)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8Q57
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 enzyme in 50 mM NaPi buffer pH 7.4 soaked with SFP for 30 seconds in a drop with 0.1 uL protein- 0.2 uL mother liquor, with the reservoir solution containing 1.5 M Ammonium sulfate, 0.1 M BIS-TRIS pH 5.5, 1% PEG 3,350
Crystal Properties Matthews coefficient Solvent content 3.18 61.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.637 α = 90 b = 87.739 β = 110.66 c = 91.008 γ = 90
Symmetry Space Group C 1 2 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 PILATUS 2M 2020-09-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97628 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 2 48.12 100 0.097 0.104 0.039 0.997 11.6 7 57013
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 2 2.05 100 0.772 0.832 0.309 0.821 7.1
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 48 54253 2688 99.85 0.18807 0.1869 0.1954 0.21151 0.2155 RANDOM 34.482
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] 1.14 0.68 -2.05 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.244 r_dihedral_angle_2_deg 12.337 r_long_range_B_refined 7.224 r_long_range_B_other 7.211 r_scangle_other 6.145 r_dihedral_angle_1_deg 5.855 r_mcangle_other 4.43 r_mcangle_it 4.429 r_scbond_it 4.291 r_scbond_other 4.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.244 r_dihedral_angle_2_deg 12.337 r_long_range_B_refined 7.224 r_long_range_B_other 7.211 r_scangle_other 6.145 r_dihedral_angle_1_deg 5.855 r_mcangle_other 4.43 r_mcangle_it 4.429 r_scbond_it 4.291 r_scbond_other 4.28 r_mcbond_it 3.514 r_mcbond_other 3.514 r_angle_refined_deg 1.65 r_angle_other_deg 0.517 r_chiral_restr 0.075 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 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 4202 Nucleic Acid Atoms Solvent Atoms 208 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement Aimless data scaling xia2 data reduction MOLREP phasing