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Crystal structure of inulosucrase from Lactobacillus reuteri 121
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YFR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 289 0.2 M Magnesium chloride hexahydrate
0.1 M Tris pH 8.5
25% w/v Polyethylene glycol 3350
Crystal Properties Matthews coefficient Solvent content 2.33 47.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.91 α = 90 b = 98.69 β = 90 c = 139.49 γ = 90
Symmetry Space Group P 21 21 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 PILATUS3 6M 2019-03-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 1.23981 SSRF BL19U1
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 1.98 50 99.9 0.135 0.141 0.039 0.999 13.8 12.7 68149
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 1.98 2.02 100 1.246 1.302 0.373 0.794 11.9
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 1.98 49.42 64716 3356 99.89 0.20265 0.20044 0.2093 0.24456 0.2515 RANDOM 36.306
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] 2.08 -2.51 0.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.887 r_dihedral_angle_4_deg 17.807 r_dihedral_angle_3_deg 13.582 r_dihedral_angle_1_deg 6.595 r_long_range_B_refined 5.275 r_long_range_B_other 5.252 r_scangle_other 3.611 r_mcangle_it 3.225 r_mcangle_other 3.225 r_scbond_it 2.358
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.887 r_dihedral_angle_4_deg 17.807 r_dihedral_angle_3_deg 13.582 r_dihedral_angle_1_deg 6.595 r_long_range_B_refined 5.275 r_long_range_B_other 5.252 r_scangle_other 3.611 r_mcangle_it 3.225 r_mcangle_other 3.225 r_scbond_it 2.358 r_scbond_other 2.357 r_mcbond_it 2.229 r_mcbond_other 2.227 r_angle_refined_deg 1.378 r_angle_other_deg 0.778 r_chiral_restr 0.081 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 8026 Nucleic Acid Atoms Solvent Atoms 400 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement HKL-3000 data scaling XDS data reduction PHASER phasing