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Structure of a Glycosyltransferase from Leptospira borgpetersenii serovar Hardjo-bovis (strain JB197)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BCV PDB entry 3BCV_B as per RosettaMR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 290 Optimization screen based on MCSG-1, condition F3: 200mM Ammonium citrate dibasic pH 5.5, 18% (w/V) PEG 3350: LpboA.19148.a.B1.PS38508 at 26.29mg/ml, seeded: cryo: 20% EG: tray 309474 e3: puck irc8-7. Protein purified in 20mM HEPES pH7, 300mM NaCl, 5% Glycerol, 1mM TCEP
Crystal Properties Matthews coefficient Solvent content 2.49 50.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.25 α = 90 b = 123.17 β = 92.44 c = 76.77 γ = 90
Symmetry Space Group P 1 21 1
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 6M 2019-05-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.00003 ALS 5.0.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.95 33.152 99 0.051 0.061 0.999 14.82 3.281 75239 33.519
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2 92.2 0.373 0.477 0.797 2.16 2.29
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 3BCV_B as per RosettaMR 1.95 33.152 1.35 75188 2075 99.03 0.1519 0.151 0.1526 0.1835 0.1848 0 34.6296
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 13.036 f_angle_d 0.743 f_chiral_restr 0.056 f_bond_d 0.007 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6165 Nucleic Acid Atoms Solvent Atoms 723 Heterogen Atoms 146
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHENIX refinement PDB_EXTRACT data extraction MR-Rosetta phasing Coot model building