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Crystal structure of Borrelia burgdorferi nicotinamidase BBE22
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 5.5 294 0.1 M Bis-Tris pH 5.5
25% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.14 42.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.343 α = 90 b = 45.21 β = 90 c = 115.212 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 EIGER2 XE 16M 2025-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.976254 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 3.2 115.21 97.8 0.191 0.993 10.2 12.4 3391
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.2 3.42 0.422 0.97 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 3.2 42.12 3197 162 97.84 0.20737 0.20445 0.2251 0.26287 0.2935 RANDOM 29.794
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 0.08 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.213 r_dihedral_angle_3_deg 20.077 r_dihedral_angle_4_deg 15.862 r_dihedral_angle_1_deg 9.328 r_long_range_B_refined 6.734 r_long_range_B_other 6.732 r_scangle_other 3.693 r_mcangle_it 3.244 r_mcangle_other 3.242 r_scbond_it 2.192
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.213 r_dihedral_angle_3_deg 20.077 r_dihedral_angle_4_deg 15.862 r_dihedral_angle_1_deg 9.328 r_long_range_B_refined 6.734 r_long_range_B_other 6.732 r_scangle_other 3.693 r_mcangle_it 3.244 r_mcangle_other 3.242 r_scbond_it 2.192 r_scbond_other 2.147 r_mcbond_it 1.932 r_mcbond_other 1.928 r_angle_refined_deg 1.567 r_angle_other_deg 1.192 r_chiral_restr 0.067 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_bond_other_d 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 1549 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling PHASER phasing