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Crystal structure of outer membrane lipoprotein carrier protein (LolA) from Francisella philomiragia (Orthorhombic P Form)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8T5J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291 Morpheus C12: 20% (v/v) Ethylene glycol; 10 % (w/v) PEG 8000; 0.02M D-Glucose; 0.05M Sodium HEPES; 0.05M MOPS (acid) pH 7.5; 0.02M D-Mannose; 0.02M D-Galactose; 0.02M L-Fucose; 0.02M D-Xylose; 0.02M N-Acetyl-D-Glucosamine; 0.2% w/v Lidocaine hydrochloride monohydrate, 0.2% w/v Procaine hydrochloride, 0.2%w/v Proparacaine hydrochloride, 0.2% w/v tetracaine hydrochloride . FrphA.20731.a.VL2.PB00125 at 13.9 mg/mL. plate 14180 well C12 drop2, Puck: PSL0901, Cryo: Direct
Crystal Properties Matthews coefficient Solvent content 1.96 37.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.272 α = 90 b = 62.107 β = 90 c = 79.454 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 9M 2024-07-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 19-ID 0.9786 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 1.7 48.93 100 0.107 0.112 0.031 0.999 14.1 13 19913
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 1.7 1.73 100 2.052 2.132 0.575 0.684 13.6
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 1.7 48.93 1.34 19860 998 99.97 0.1865 0.1843 0.1906 0.2269 0.2278
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 15.618 f_angle_d 1.014 f_chiral_restr 0.066 f_bond_d 0.01 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1213 Nucleic Acid Atoms Solvent Atoms 92 Heterogen Atoms 18
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing