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Structural basis for the acyl chain selectivity and mechanism of UDP-N-acetylglucosamine Acyltransferase
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, HANGING DROP 5.6 291 0.8-1.4 Na/K phosphate, pH 5.6-6.3, 30%-35% Dimethyl Sulfoxide(DMSO), VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.72 54.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.143 α = 90 b = 97.143 β = 90 c = 97.143 γ = 90
Symmetry Space Group P 21 3
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 2006-04-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
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 1.74 50 95.1 0.047 35.5 3.3 30085 3
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) 1.74 1.8 93.1 0.178 3.5 2892
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) 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 1.74 23.56 3 30044 1517 95.13 0.188 0.186 0.1845 0.232 0.2286 RANDOM 21.214
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 36.331 r_dihedral_angle_4_deg 17.47 r_dihedral_angle_3_deg 11.808 r_dihedral_angle_1_deg 5.679 r_scangle_it 1.884 r_scbond_it 1.115 r_angle_refined_deg 1.096 r_mcangle_it 0.588 r_mcbond_it 0.385 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.331 r_dihedral_angle_4_deg 17.47 r_dihedral_angle_3_deg 11.808 r_dihedral_angle_1_deg 5.679 r_scangle_it 1.884 r_scbond_it 1.115 r_angle_refined_deg 1.096 r_mcangle_it 0.588 r_mcbond_it 0.385 r_nbtor_refined 0.304 r_nbd_refined 0.18 r_symmetry_vdw_refined 0.153 r_symmetry_hbond_refined 0.117 r_xyhbond_nbd_refined 0.102 r_chiral_restr 0.065 r_bond_refined_d 0.007 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1974 Nucleic Acid Atoms Solvent Atoms 412 Heterogen Atoms 55
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction