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Crystal structure analysis of LpxA, a UDP-N-acetylglucosamine acyltransferase from Bacteroides fragilis 9343
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 2.31 46.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 149.051 α = 90 b = 149.051 β = 90 c = 149.051 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 1.9 105.39 99.9 0.051 35.3 10.6 45045 45045 -3 22.9
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 1.94 99 0.554 4.9 10.3 2836
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 42699 42699 2277 99.92 0.15705 0.15521 0.1668 0.19241 0.2007 RANDOM 26.097
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 36.142 r_dihedral_angle_4_deg 22.279 r_dihedral_angle_3_deg 12.226 r_long_range_B_refined 6.826 r_long_range_B_other 6.826 r_dihedral_angle_1_deg 6.741 r_scangle_other 5.288 r_scbond_it 3.549 r_scbond_other 3.548 r_mcangle_other 2.802
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.142 r_dihedral_angle_4_deg 22.279 r_dihedral_angle_3_deg 12.226 r_long_range_B_refined 6.826 r_long_range_B_other 6.826 r_dihedral_angle_1_deg 6.741 r_scangle_other 5.288 r_scbond_it 3.549 r_scbond_other 3.548 r_mcangle_other 2.802 r_mcangle_it 2.801 r_mcbond_it 2.229 r_mcbond_other 2.221 r_angle_refined_deg 1.852 r_angle_other_deg 1.228 r_chiral_restr 0.108 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 453 Heterogen Atoms 54
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement XDS data reduction Aimless data scaling