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Chimeric Glycosyltransferase LanGT2S8Ac, TDP complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2P6P LanGT2, wild type
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 278 34% PEG 3350
0.17 M MgCl2
16 mM L-proline
0.1 M HEPES/NaOH, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 278K
Crystal Properties Matthews coefficient Solvent content 2.24 45.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.693 α = 78.78 b = 58.669 β = 70.16 c = 63.66 γ = 86.77
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2013-06-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.000 SLS X06SA
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 46.37 95.5 0.047 11.8 47043 44926 2 2.5
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 THROUGHOUT LanGT2, wild type 2 46.37 47043 42662 2264 94.45 0.19896 0.19896 0.19722 0.1954 0.23122 0.2292 RANDOM 35.354
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] -0.06 0.66 -1.16 -1.67 -0.98 0.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.521 r_dihedral_angle_4_deg 18.085 r_dihedral_angle_3_deg 14.384 r_dihedral_angle_1_deg 5.047 r_long_range_B_refined 4.204 r_mcangle_it 1.498 r_angle_refined_deg 1.182 r_scbond_it 0.906 r_mcbond_it 0.843 r_chiral_restr 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.521 r_dihedral_angle_4_deg 18.085 r_dihedral_angle_3_deg 14.384 r_dihedral_angle_1_deg 5.047 r_long_range_B_refined 4.204 r_mcangle_it 1.498 r_angle_refined_deg 1.182 r_scbond_it 0.906 r_mcbond_it 0.843 r_chiral_restr 0.08 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined 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_it r_scangle_other 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 5295 Nucleic Acid Atoms Solvent Atoms 207 Heterogen Atoms 51
Software Software Software Name Purpose MOLREP phasing REFMAC refinement XDS data reduction SCALA data scaling