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Crystal structure of YeGT glycosyltransferase with bound UDP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4MIX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 100mM HEPES pH 7.5, 500mM sodium acetate, 50mM cadmium sulfate
Crystal Properties Matthews coefficient Solvent content 2.76 55.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.13 α = 90 b = 114.546 β = 89.987 c = 69.376 γ = 90
Symmetry Space Group P 1 21 1
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 2017-11-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 1.0000 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) 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 1.12 47.13 92.7 0.132 0.023 0.999 18 30.3 213705
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.12 1.22 2.038 0.479 0.39 1.7 18.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.123 47.13 213699 10763 76.61 0.154 0.1533 0.1685 0.1899 17.643
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] -8.967 -0.612 13.568 -4.601
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.982 r_dihedral_angle_other_3_deg 18.238 r_dihedral_angle_4_deg 17.08 r_dihedral_angle_3_deg 11.238 r_dihedral_angle_1_deg 5.678 r_lrange_it 2.748 r_lrange_other 2.046 r_angle_other_deg 1.231 r_angle_refined_deg 1.196 r_mcangle_it 1.157
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.982 r_dihedral_angle_other_3_deg 18.238 r_dihedral_angle_4_deg 17.08 r_dihedral_angle_3_deg 11.238 r_dihedral_angle_1_deg 5.678 r_lrange_it 2.748 r_lrange_other 2.046 r_angle_other_deg 1.231 r_angle_refined_deg 1.196 r_mcangle_it 1.157 r_mcangle_other 1.156 r_scangle_it 1.146 r_scangle_other 1.146 r_scbond_it 1.036 r_scbond_other 0.96 r_mcbond_it 0.832 r_mcbond_other 0.829 r_rigid_bond_restr 0.714 r_nbd_refined 0.184 r_symmetry_nbd_other 0.167 r_nbtor_refined 0.159 r_symmetry_nbd_refined 0.143 r_nbd_other 0.12 r_metal_ion_refined 0.117 r_xyhbond_nbd_refined 0.104 r_symmetry_xyhbond_nbd_refined 0.094 r_symmetry_nbtor_other 0.075 r_symmetry_xyhbond_nbd_other 0.058 r_symmetry_metal_ion_refined 0.058 r_chiral_restr 0.055 r_bond_other_d 0.01 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4369 Nucleic Acid Atoms Solvent Atoms 871 Heterogen Atoms 132
Software Software Software Name Purpose REFMAC refinement MxCuBE data collection autoPROC data processing PHASER phasing STARANISO data scaling Coot model building autoPROC data reduction