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Crystal structure of OspA ST1 from B. burgdorferi bound to monoclonal antibody LA-2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FJ1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293.15 15 mg/mL, 0.1 M Magnesium Acetate tetrahydrate and 10% (w/v) PEG 3350; cryo 25%(v/v) Glycerol
Crystal Properties Matthews coefficient Solvent content 2.7 54.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.555 α = 90 b = 68.555 β = 90 c = 619.736 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 EIGER X 9M 2023-07-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.9537 CLSI 08ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 1.85 68.86 100 0.125 0.129 0.029 0.999 17 19.4 139556
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.88 100 2.821 2.889 0.661 0.304 1 18.8
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.85 59.1 139278 6937 99.985 0.204 0.2023 0.1932 0.2333 0.2261 Random 40.945
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] -2.614 -2.614 5.227
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 20.678 r_dihedral_angle_3_deg 14.778 r_dihedral_angle_6_deg 14.06 r_dihedral_angle_1_deg 7.087 r_lrange_it 3.895 r_lrange_other 3.885 r_mcangle_it 2.251 r_mcangle_other 2.251 r_scangle_it 2.209 r_scangle_other 2.209
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 20.678 r_dihedral_angle_3_deg 14.778 r_dihedral_angle_6_deg 14.06 r_dihedral_angle_1_deg 7.087 r_lrange_it 3.895 r_lrange_other 3.885 r_mcangle_it 2.251 r_mcangle_other 2.251 r_scangle_it 2.209 r_scangle_other 2.209 r_mcbond_it 1.604 r_mcbond_other 1.604 r_scbond_it 1.592 r_scbond_other 1.592 r_angle_refined_deg 1.282 r_angle_other_deg 0.452 r_symmetry_nbd_other 0.205 r_nbd_refined 0.192 r_symmetry_xyhbond_nbd_refined 0.184 r_xyhbond_nbd_refined 0.182 r_ncsr_local_group_3 0.175 r_nbtor_refined 0.17 r_ncsr_local_group_2 0.149 r_nbd_other 0.142 r_ncsr_local_group_1 0.136 r_symmetry_nbtor_other 0.084 r_symmetry_nbd_refined 0.073 r_chiral_restr 0.062 r_symmetry_xyhbond_nbd_other 0.062 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10205 Nucleic Acid Atoms Solvent Atoms 563 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing