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Crystal structure of universal stress protein E from Proteus mirabilis in complex with UDP-3-O-[(3R)-3-hydroxytetradecanoyl]-N-acetyl-alpha-glucosamine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3OLQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 289 0.2 ul of 12 mg/ml protein in 10mM HEPES, 500mM NaCl pH 7.5 were mixed with 0.2 ul of the Quiagen Cryos Suite condition #50 (1.36 M Ammonium Sulfate, 0.085 M MES pH 6.5, 8.5% Dioxane, 15% Glycerol) and equilibrated against the mother liquor in 96 Well 2 drop Crystallization Plate (MRC)
Crystal Properties Matthews coefficient Solvent content 3 59.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.877 α = 90 b = 107.877 β = 90 c = 74.923 γ = 90
Symmetry Space Group P 43 21 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 CCD MARMOSAIC 225 mm CCD Beryllium Lenses 2014-07-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 50 99.6 0.08 0.087 0.033 9.5 6.6 41254 -3 29
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 1.83 98.7 0.892 0.976 0.389 0.75 1.9 6.1 2017
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 3OLQ 1.8 50 39066 2019 98.99 0.1736 0.1721 0.182 0.2018 0.2113 RANDOM 35.365
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] -1.01 -1.01 2.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.567 r_dihedral_angle_4_deg 17.273 r_dihedral_angle_3_deg 13.234 r_dihedral_angle_1_deg 5.457 r_mcangle_it 1.792 r_angle_refined_deg 1.453 r_mcbond_other 1.166 r_mcbond_it 1.165 r_angle_other_deg 0.776 r_chiral_restr 0.086
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.567 r_dihedral_angle_4_deg 17.273 r_dihedral_angle_3_deg 13.234 r_dihedral_angle_1_deg 5.457 r_mcangle_it 1.792 r_angle_refined_deg 1.453 r_mcbond_other 1.166 r_mcbond_it 1.165 r_angle_other_deg 0.776 r_chiral_restr 0.086 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2448 Nucleic Acid Atoms Solvent Atoms 319 Heterogen Atoms 73
Software Software Software Name Purpose BLU-MAX data collection HKL-3000 data reduction HKL-3000 data scaling HKL-3000 phasing MOLREP phasing REFMAC refinement Coot model building PDB_EXTRACT data extraction