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Crystal structure of Borrelia burgdorferi BB0158
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 4.6 294 0.2 M ammonium sulfate
0.1 M sodium acetate (pH 4.6)
20% PEG 2000 MME
Crystal Properties Matthews coefficient Solvent content 2.42 49.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.063 α = 90 b = 81.774 β = 109.381 c = 80.801 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 PILATUS3 S 6M 2022-10-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.918400 BESSY 14.1
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 2.4 44.97 99.3 0.074 0.998 15 6.9 35959
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 2.4 2.49 0.403 0.938 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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.4 44.97 35949 1821 99.255 0.217 0.213 0.2172 0.2973 0.299 48.838
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] -0.002 0.004 -0.003 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.938 r_dihedral_angle_3_deg 17.399 r_lrange_it 9.115 r_lrange_other 9.109 r_dihedral_angle_1_deg 7.818 r_scangle_it 6.417 r_scangle_other 6.417 r_mcangle_it 6.044 r_mcangle_other 6.044 r_scbond_it 4.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.938 r_dihedral_angle_3_deg 17.399 r_lrange_it 9.115 r_lrange_other 9.109 r_dihedral_angle_1_deg 7.818 r_scangle_it 6.417 r_scangle_other 6.417 r_mcangle_it 6.044 r_mcangle_other 6.044 r_scbond_it 4.24 r_scbond_other 4.206 r_mcbond_it 4.115 r_mcbond_other 4.113 r_angle_other_deg 2.287 r_angle_refined_deg 1.567 r_symmetry_nbd_refined 0.343 r_nbd_other 0.303 r_symmetry_nbd_other 0.222 r_nbd_refined 0.21 r_nbtor_refined 0.168 r_xyhbond_nbd_refined 0.158 r_symmetry_xyhbond_nbd_refined 0.103 r_symmetry_nbtor_other 0.072 r_chiral_restr 0.065 r_symmetry_xyhbond_nbd_other 0.064 r_bond_other_d 0.034 r_bond_refined_d 0.008 r_gen_planes_other 0.008 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6473 Nucleic Acid Atoms Solvent Atoms 248 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing