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Crystal structure of TDP-fucosamine acetyltransferase (WecD)- complex with acetyl-CoA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FS5 PDB entry 2FS5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 298 100 mM sodium acetate, 10 mM zinc sulfate, 2 mM acetyl-CoA, 5 mM TDP, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.73 54.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.9 α = 90 b = 84.9 β = 90 c = 154.122 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 ADSC QUANTUM 315 2005-03-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.1 NSLS X29A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.66 39 97.3 0.053 18 6.2 65489
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 2FS5 1.66 39 65417 62158 3259 97.96 0.20351 0.20248 0.2028 0.2232 0.2238 RANDOM 25.256
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] 0.53 0.53 -1.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.06 r_dihedral_angle_4_deg 13.291 r_dihedral_angle_3_deg 12.46 r_dihedral_angle_1_deg 5.604 r_scangle_it 3.31 r_scbond_it 2.213 r_mcangle_it 1.321 r_angle_refined_deg 1.298 r_mcbond_it 0.873 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.06 r_dihedral_angle_4_deg 13.291 r_dihedral_angle_3_deg 12.46 r_dihedral_angle_1_deg 5.604 r_scangle_it 3.31 r_scbond_it 2.213 r_mcangle_it 1.321 r_angle_refined_deg 1.298 r_mcbond_it 0.873 r_nbtor_refined 0.302 r_nbd_refined 0.201 r_symmetry_vdw_refined 0.185 r_symmetry_hbond_refined 0.153 r_xyhbond_nbd_refined 0.142 r_chiral_restr 0.084 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3384 Nucleic Acid Atoms Solvent Atoms 412 Heterogen Atoms 102
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing