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Crystal structure of NodZ alpha-1,6-fucosyltransferase soaked with GDP-fucose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HHC PDB ENTRY 2HHC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 350 mM potassium sodium tartrate
100 mM MES pH 6.5
50 mM MgCl2
, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.88 57.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.8 α = 90 b = 128.8 β = 90 c = 91.1 γ = 120
Symmetry Space Group P 65 2 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 MARMOSAIC 225 mm CCD 2011-04-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 0.97242 APS 22-BM
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 2.35 50 99.9 0.091 20.5 10.6 19194 19190 -3 56.6
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 2.35 2.43 100 0.656 3.3 10.1 1878
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 (All) 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 R-FREE PDB ENTRY 2HHC 2.35 50 19194 19048 1030 99.3 0.2124 0.2124 0.21 0.2117 0.2569 0.2525 RANDOM 56
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] -0.6 -0.3 -0.6 0.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.448 r_dihedral_angle_4_deg 18.094 r_dihedral_angle_3_deg 15.493 r_scangle_it 6.279 r_dihedral_angle_1_deg 5.978 r_scbond_it 4.203 r_mcangle_it 1.671 r_angle_refined_deg 1.491 r_angle_other_deg 0.876 r_mcbond_it 0.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.448 r_dihedral_angle_4_deg 18.094 r_dihedral_angle_3_deg 15.493 r_scangle_it 6.279 r_dihedral_angle_1_deg 5.978 r_scbond_it 4.203 r_mcangle_it 1.671 r_angle_refined_deg 1.491 r_angle_other_deg 0.876 r_mcbond_it 0.86 r_mcbond_other 0.169 r_chiral_restr 0.095 r_bond_refined_d 0.018 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2345 Nucleic Acid Atoms Solvent Atoms 82 Heterogen Atoms 34
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction SERGUI data collection HKL-3000 data reduction HKL-3000 data scaling PHASER phasing