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Crystal structure of metal-dependent class II sulfofructosephosphate aldolase from Hafnia paralvei HpSqiA-Zn in complex with dihydroxyacetone phosphate (DHAP)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8Q58
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 A crystal of the DHAP complex grew from 14 mg mL-1 enzyme in 50 mM Tris buffer pH 7.4 in a drop with 0.15 uL protein to 0.15 uL mother liquor soaked with SFP for 2 min, with the reservoir solution containing 25% PEG 1,500 w/v, 0.1 M SPG (succinic acid, propionate, glycine) buffer pH 7
Crystal Properties Matthews coefficient Solvent content 2.44 49.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.605 α = 90 b = 87.669 β = 90 c = 103.3 γ = 90
Symmetry Space Group I 2 2 2
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 2020-08-10 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 2.8 34.22 99.9 0.101 0.105 0.029 0.997 17.7 12.7 7522
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 2.8 2.95 100 0.439 0.456 0.123 0.971 13.4
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 2.8 34 7129 382 99.75 0.21133 0.20793 0.2115 0.27408 0.2724 RANDOM 46.956
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] -1.51 2.32 -0.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.757 r_long_range_B_refined 9.023 r_long_range_B_other 9.021 r_mcangle_other 7.019 r_mcangle_it 7.018 r_scangle_other 6.413 r_dihedral_angle_1_deg 6.224 r_dihedral_angle_2_deg 4.952 r_mcbond_it 4.547 r_mcbond_other 4.547
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.757 r_long_range_B_refined 9.023 r_long_range_B_other 9.021 r_mcangle_other 7.019 r_mcangle_it 7.018 r_scangle_other 6.413 r_dihedral_angle_1_deg 6.224 r_dihedral_angle_2_deg 4.952 r_mcbond_it 4.547 r_mcbond_other 4.547 r_scbond_it 4.209 r_scbond_other 4.199 r_angle_refined_deg 1.251 r_angle_other_deg 0.447 r_chiral_restr 0.056 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 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 1932 Nucleic Acid Atoms Solvent Atoms 6 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement Aimless data scaling xia2 data reduction MOLREP phasing