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Carbohydrate-binding module 32 of LnbB from Bifidobacterium bifidum, ligand free form, multiple small-wedge data set
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 TRIS-HCL, AMMONIUM SULFATE, PH 8.0
Crystal Properties Matthews coefficient Solvent content 1.96 37.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.78 α = 90 b = 54.78 β = 90 c = 202.9 γ = 90
Symmetry Space Group P 41 21 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 6M 2024-10-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 1.0000 SPring-8 BL45XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 50 99.9 0.1823 0.1844 0.978 8.84 45.5 21990 17.86
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.09 100 1.038 1.051 0.618 0.82 40.4
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 48.25 20822 1071 99.96 0.22527 0.22447 0.2354 0.24034 0.2496 RANDOM 21.56
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] 2.17 2.17 -4.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.705 r_dihedral_angle_1_deg 7.16 r_long_range_B_refined 5.195 r_long_range_B_other 5.172 r_dihedral_angle_2_deg 3.915 r_scangle_other 3.474 r_mcangle_it 3.028 r_mcangle_other 3.027 r_scbond_it 2.061 r_scbond_other 2.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.705 r_dihedral_angle_1_deg 7.16 r_long_range_B_refined 5.195 r_long_range_B_other 5.172 r_dihedral_angle_2_deg 3.915 r_scangle_other 3.474 r_mcangle_it 3.028 r_mcangle_other 3.027 r_scbond_it 2.061 r_scbond_other 2.06 r_mcbond_it 1.752 r_mcbond_other 1.751 r_angle_refined_deg 1.505 r_angle_other_deg 0.511 r_chiral_restr 0.069 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 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 2430 Nucleic Acid Atoms Solvent Atoms 136 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling MOLREP phasing