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glycosyltransferase in complex with UDP and ST
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7ERY apo form of this protein
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 20% PEG 4000 and 0.1 M HEPES pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.31 46.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.843 α = 90 b = 83.042 β = 90 c = 109.167 γ = 90
Symmetry Space Group P 21 21 21
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 2019-12-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.978 SSRF BL18U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.66 46.09 99.9 0.089 0.996 9 5.9 55463
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.66 1.69 96.8 1.087 0.499 3.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT apo form of this protein 1.66 46.089 55377 2734 99.775 0.18 0.1788 0.1891 0.2043 0.2124 29.627
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] 1.38 -0.4 -0.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.525 r_dihedral_angle_4_deg 16.521 r_dihedral_angle_3_deg 12.735 r_dihedral_angle_1_deg 6.444 r_lrange_it 6.311 r_lrange_other 6.19 r_scangle_it 1.694 r_scangle_other 1.693 r_mcangle_it 1.626 r_mcangle_other 1.625
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.525 r_dihedral_angle_4_deg 16.521 r_dihedral_angle_3_deg 12.735 r_dihedral_angle_1_deg 6.444 r_lrange_it 6.311 r_lrange_other 6.19 r_scangle_it 1.694 r_scangle_other 1.693 r_mcangle_it 1.626 r_mcangle_other 1.625 r_angle_refined_deg 1.438 r_angle_other_deg 1.351 r_scbond_it 0.999 r_scbond_other 0.999 r_mcbond_it 0.902 r_mcbond_other 0.902 r_dihedral_angle_other_2_deg 0.444 r_nbd_refined 0.202 r_nbd_other 0.191 r_symmetry_xyhbond_nbd_refined 0.176 r_symmetry_nbd_other 0.172 r_symmetry_nbd_refined 0.17 r_nbtor_refined 0.159 r_xyhbond_nbd_refined 0.116 r_symmetry_nbtor_other 0.076 r_chiral_restr 0.072 r_symmetry_xyhbond_nbd_other 0.011 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3122 Nucleic Acid Atoms Solvent Atoms 397 Heterogen Atoms 59
Software Software Software Name Purpose REFMAC refinement DIALS data reduction PHASER phasing DIALS data scaling