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Crystal structure analysis of LpxA, a UDP-N-acetylglucosamine acyltransferase from Bacteroides fragilis 9343 with UDP-GlcNAc
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LXA PDB entry 1LXA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 28 % PEG600, 200 mM Calcium Acetate, 100 mM Sodium Cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.32 47.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 149.403 α = 90 b = 149.403 β = 90 c = 149.403 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 CCD ADSC QUANTUM 315 Rh coated flat mirror 2014-07-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 1.12709 SSRL BL7-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.9 105.64 99.9 0.052 30 7.1 45186 45186 -3 18.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.95 99.5 0.357 5.6 7.1 2959
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1LXA 1.9 38 42852 42852 2289 99.85 0.14928 0.14739 0.1597 0.18513 0.1933 RANDOM 21.123
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 r_dihedral_angle_2_deg 36.379 r_dihedral_angle_4_deg 20.874 r_dihedral_angle_3_deg 12.584 r_dihedral_angle_1_deg 6.724 r_long_range_B_refined 6.366 r_long_range_B_other 6.097 r_scangle_other 4.49 r_scbond_it 3.026 r_scbond_other 3.025 r_mcangle_other 2.285
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.379 r_dihedral_angle_4_deg 20.874 r_dihedral_angle_3_deg 12.584 r_dihedral_angle_1_deg 6.724 r_long_range_B_refined 6.366 r_long_range_B_other 6.097 r_scangle_other 4.49 r_scbond_it 3.026 r_scbond_other 3.025 r_mcangle_other 2.285 r_mcangle_it 2.284 r_angle_refined_deg 1.798 r_mcbond_it 1.742 r_mcbond_other 1.726 r_angle_other_deg 1.231 r_chiral_restr 0.105 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 r_bond_other_d 0.006 r_gen_planes_other 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3894 Nucleic Acid Atoms Solvent Atoms 517 Heterogen Atoms 86
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement XDS data reduction Aimless data scaling