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Crystal structure of Borrelia recurrentis variable large protein VlpA1 (VmpA1)
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 8 294 22% Jeffamine ED-2001
3% PEG 3350
Crystal Properties Matthews coefficient Solvent content 1.98 37.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.891 α = 90 b = 77.723 β = 90 c = 170.563 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 2024-11-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.953738 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 2.45 170.56 97.3 0.113 0.997 13.8 13.1 18874
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.45 2.55 0.967 5.5
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 2.45 85.28 17881 932 97.22 0.20125 0.19749 0.2077 0.2707 0.2782 RANDOM 38.837
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] -0.02 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.354 r_dihedral_angle_4_deg 22.973 r_dihedral_angle_3_deg 19.455 r_long_range_B_refined 7.831 r_long_range_B_other 7.829 r_dihedral_angle_1_deg 7.365 r_scangle_other 5.433 r_mcangle_it 4.608 r_mcangle_other 4.608 r_scbond_it 3.378
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.354 r_dihedral_angle_4_deg 22.973 r_dihedral_angle_3_deg 19.455 r_long_range_B_refined 7.831 r_long_range_B_other 7.829 r_dihedral_angle_1_deg 7.365 r_scangle_other 5.433 r_mcangle_it 4.608 r_mcangle_other 4.608 r_scbond_it 3.378 r_scbond_other 3.377 r_mcbond_it 2.988 r_mcbond_other 2.982 r_angle_refined_deg 1.547 r_angle_other_deg 1.265 r_chiral_restr 0.061 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.002 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 4343 Nucleic Acid Atoms Solvent Atoms 143 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling PHASER phasing