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Crystal structure of NodZ alpha-1,6-fucosyltransferase co-crystallized with GDP
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 6.5 293 400 mM KH2PO4
100 mM MES pH 6.5
5 mM MgCl2
2 mM GDP
1 mM Chitopentaose, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.79 55.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.9 α = 90 b = 123.9 β = 90 c = 95.2 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 300 mm CCD 2010-11-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.00000 APS 22-ID
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 1.98 50 99.9 0.119 16.6 9.8 30810 30783 -3 24.6
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 1.98 2.05 99.9 0.706 9.4 3003
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 1.98 46.73 30528 30451 1103 99.75 0.1737 0.1737 0.1721 0.1826 0.2173 0.2334 RANDOM 32.892
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] -1.4 -0.7 -1.4 2.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.174 r_dihedral_angle_4_deg 19.109 r_dihedral_angle_3_deg 15.575 r_dihedral_angle_1_deg 6.023 r_scangle_it 5.609 r_scbond_it 3.819 r_mcangle_it 1.846 r_angle_refined_deg 1.698 r_mcbond_it 1.018 r_angle_other_deg 0.959
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.174 r_dihedral_angle_4_deg 19.109 r_dihedral_angle_3_deg 15.575 r_dihedral_angle_1_deg 6.023 r_scangle_it 5.609 r_scbond_it 3.819 r_mcangle_it 1.846 r_angle_refined_deg 1.698 r_mcbond_it 1.018 r_angle_other_deg 0.959 r_mcbond_other 0.273 r_chiral_restr 0.107 r_bond_refined_d 0.019 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 2333 Nucleic Acid Atoms Solvent Atoms 199 Heterogen Atoms 43
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