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Crystal structure of Borrelia burgdorferi BB0238-BB0323 complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6RJX experimental model PDB 8P33
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 294 0.01 M NiCl2 6H2O
0.1 M Tris pH 8.5
20% PEG 2000 MME
Crystal Properties Matthews coefficient Solvent content 2.61 52.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.76 α = 90 b = 130.76 β = 90 c = 38.943 γ = 120
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 2022-12-09 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 3.6 42.8 99.9 0.104 0.999 18.9 19.9 4620
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 3.6 3.94 100 0.541 0.979 6.9
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 3.6 37.78 4380 230 99.89 0.20573 0.19916 0.2491 0.33509 0.3345 RANDOM 114.559
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] -0.08 -0.04 -0.08 0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.248 r_dihedral_angle_3_deg 25.054 r_long_range_B_refined 22.513 r_long_range_B_other 22.49 r_dihedral_angle_4_deg 17.258 r_scangle_other 15.761 r_mcangle_other 14.286 r_mcangle_it 14.285 r_scbond_it 9.731 r_scbond_other 9.727
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.248 r_dihedral_angle_3_deg 25.054 r_long_range_B_refined 22.513 r_long_range_B_other 22.49 r_dihedral_angle_4_deg 17.258 r_scangle_other 15.761 r_mcangle_other 14.286 r_mcangle_it 14.285 r_scbond_it 9.731 r_scbond_other 9.727 r_mcbond_it 9.217 r_mcbond_other 9.174 r_dihedral_angle_1_deg 6.333 r_angle_refined_deg 1.445 r_angle_other_deg 1.214 r_chiral_restr 0.052 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.004 r_gen_planes_other 0.002 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 2223 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing