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Crystal structure of class II SFP aldolase from Yersinia aldovae (YaSqiA-Zn-SO4) with bound sulfate ions
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5UCK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 Protein at 16 mg mL-1 in 50 mM NaPi, 300 mM NaCl buffer pH 7.4, using a drop containing 0.6 uL protein and 0.5 uL mother liquor, the latter comprising 1.5 M ammonium sulfate, 0.1 M NaCl, 0.1 M BIS-TRIS pH 6.5
Crystal Properties Matthews coefficient Solvent content 3.08 60.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.734 α = 90 b = 87.525 β = 107.73 c = 104.312 γ = 90
Symmetry Space Group I 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 PILATUS3 2M 2020-01-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
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 1.7 61.5 100 0.073 0.079 0.03 0.999 12.9 7.1 85319
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 1.7 1.73 99.9 1.181 1.276 0.481 0.752 6.9
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 1.7 61.01 81063 4241 99.95 0.18579 0.18477 0.1963 0.20522 0.2133 RANDOM 28.012
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] -1.35 0.06 -1.26 2.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.32 r_dihedral_angle_2_deg 9.819 r_long_range_B_refined 6.851 r_long_range_B_other 6.85 r_dihedral_angle_1_deg 5.73 r_scangle_other 5.652 r_scbond_it 3.892 r_scbond_other 3.891 r_mcangle_it 3.619 r_mcangle_other 3.618
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.32 r_dihedral_angle_2_deg 9.819 r_long_range_B_refined 6.851 r_long_range_B_other 6.85 r_dihedral_angle_1_deg 5.73 r_scangle_other 5.652 r_scbond_it 3.892 r_scbond_other 3.891 r_mcangle_it 3.619 r_mcangle_other 3.618 r_mcbond_it 2.846 r_mcbond_other 2.843 r_angle_refined_deg 1.511 r_angle_other_deg 0.52 r_chiral_restr 0.083 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 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 4181 Nucleic Acid Atoms Solvent Atoms 271 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement Aimless data scaling xia2 data reduction MOLREP phasing