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Crystal structure of Borrelia burgdorferi CspZ-YACS
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4BG0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 294 2.2 M ammonium sulfate
0.1 M HEPES 7.5
2% PEG 400
Crystal Properties Matthews coefficient Solvent content 2.14 42.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 31.551 α = 90 b = 41.677 β = 90 c = 162.812 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 PILATUS3 S 6M 2023-03-17 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 1.95 41.68 99.9 0.095 0.998 18.1 12.5 16483
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 1.95 2 100 0.693 0.971 3.6 13.3
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 1.95 40.74 14928 839 95.82 0.2318 0.23047 0.2422 0.2551 0.2684 RANDOM 30.034
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] 4.51 -1.2 -3.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.904 r_dihedral_angle_4_deg 18.961 r_dihedral_angle_3_deg 16.959 r_long_range_B_refined 8.53 r_long_range_B_other 8.426 r_dihedral_angle_1_deg 6.17 r_scangle_other 5.554 r_mcangle_it 4.589 r_mcangle_other 4.587 r_scbond_it 3.593
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.904 r_dihedral_angle_4_deg 18.961 r_dihedral_angle_3_deg 16.959 r_long_range_B_refined 8.53 r_long_range_B_other 8.426 r_dihedral_angle_1_deg 6.17 r_scangle_other 5.554 r_mcangle_it 4.589 r_mcangle_other 4.587 r_scbond_it 3.593 r_scbond_other 3.544 r_mcbond_it 2.916 r_mcbond_other 2.903 r_angle_refined_deg 1.571 r_angle_other_deg 1.412 r_chiral_restr 0.084 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 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 1738 Nucleic Acid Atoms Solvent Atoms 179 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing