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Activity and Crystal Structure of Francisella novicida UDP-N-Acetylglucosamine Acyltransferase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LXA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.2M Lithium sulfate, 0.1M Tris HCl pH 8.5, 30% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.5 50.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.38 α = 90 b = 105.38 β = 90 c = 285.79 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV++ 2009-03-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.06 19.49 100 8.02 4 35991
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.06 2.11
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 1LXA 2.06 18.95 35986 1894 100 0.21225 0.20978 0.2088 0.25968 0.2572 RANDOM 29.858
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] 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.273 r_dihedral_angle_4_deg 19.061 r_dihedral_angle_3_deg 13.876 r_dihedral_angle_1_deg 5.862 r_scangle_it 2.219 r_scbond_it 1.349 r_angle_refined_deg 1.112 r_mcangle_it 0.961 r_mcbond_it 0.545 r_nbtor_refined 0.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.273 r_dihedral_angle_4_deg 19.061 r_dihedral_angle_3_deg 13.876 r_dihedral_angle_1_deg 5.862 r_scangle_it 2.219 r_scbond_it 1.349 r_angle_refined_deg 1.112 r_mcangle_it 0.961 r_mcbond_it 0.545 r_nbtor_refined 0.299 r_nbd_refined 0.188 r_symmetry_vdw_refined 0.173 r_symmetry_hbond_refined 0.14 r_xyhbond_nbd_refined 0.119 r_chiral_restr 0.073 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4200 Nucleic Acid Atoms Solvent Atoms 379 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data scaling