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Crystal structure of outer membrane lipoprotein carrier protein (LolA) from Borrelia burgdorferi (steric acid bound)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7TPM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291 Berkeley E4: 1500 mM Ammonium sulfate, 100 mM Hepes pH 7.5. BobuA.17454.a.DH3.PK00001 at 10 mg/mL. plate 13170, well E4 drop 3. Puck: PSL-1107, Cryo: 2.5M lithium sulfate, Large mass of electron density in the binding pocket that appeared to be a fatty acid from the expression host. Modelled as steric acid
Crystal Properties Matthews coefficient Solvent content 3.26 62.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.291 α = 90 b = 122.291 β = 90 c = 122.291 γ = 90
Symmetry Space Group P 41 3 2
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 9M 2023-03-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 19-ID 0.9795 NSLS-II 19-ID
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 1.8 49.93 100 0.077 0.078 0.012 1 30.1 39.1 29577
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 1.8 1.84 100 2.755 2.791 0.443 0.77 39.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.8 28.82 1.1 29510 1475 99.97 0.1982 0.1962 0.2018 0.2362 0.2334
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 11.196 f_angle_d 1.151 f_chiral_restr 0.065 f_bond_d 0.011 f_plane_restr 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1507 Nucleic Acid Atoms Solvent Atoms 161 Heterogen Atoms 65
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing