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Crystal structure of carrageenan sulfatase Bt3731_S1_30A from human gut bacterium Bacteroides thetaiotaomicron VPI-3731
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold The same protein sequence is used to generate search model.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.2 291 0.2 M Sodium Chloride; 0.1 M Na2HPO4: Citric Acid, pH 4.2; 20 % (w/v) PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.26 45.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.97 α = 90 b = 115.928 β = 94.72 c = 177.205 γ = 90
Symmetry Space Group P 1 21 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 6M 2021-12-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.03321 PETRA III, DESY P11
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 2.4 176.6 99.2 0.188 0.209 0.089 0.99 4.7 5.3 82713
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 2.4 2.45 99.8 0.745 0.831 0.36 0.862 5.4
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 2.4 176.6 78674 4010 99.13 0.19501 0.19223 0.2187 0.24857 0.2616 RANDOM 40.036
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] 0.03 -0.15 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.107 r_long_range_B_other 13.103 r_long_range_B_refined 13.101 r_dihedral_angle_2_deg 11.859 r_scangle_other 9.732 r_mcangle_it 8.76 r_mcangle_other 8.759 r_dihedral_angle_1_deg 8.609 r_scbond_it 6.817 r_scbond_other 6.817
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.107 r_long_range_B_other 13.103 r_long_range_B_refined 13.101 r_dihedral_angle_2_deg 11.859 r_scangle_other 9.732 r_mcangle_it 8.76 r_mcangle_other 8.759 r_dihedral_angle_1_deg 8.609 r_scbond_it 6.817 r_scbond_other 6.817 r_mcbond_it 6.034 r_mcbond_other 6.031 r_angle_refined_deg 2.369 r_angle_other_deg 0.802 r_chiral_restr 0.111 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 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 16004 Nucleic Acid Atoms Solvent Atoms 274 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement Aimless data scaling DIALS data reduction PHASER phasing