☰ Navigation Tabs
Glycosyltransferase in complex with UDP and STB
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7ERY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 100 mM HEPES-NaOH buffer pH 6.5 and 20% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.48 50.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.482 α = 90 b = 83.173 β = 90 c = 109.391 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 2020-10-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.97915 SSRF BL18U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.92 109.39 99.7 0.055 0.066 0.036 0.999 14.5 6.2 38620
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.92 1.97 1.852 2.264 1.282 0.626 5.1
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 7ERY 1.92 66.297 38555 1952 99.564 0.19 0.1885 0.194 0.2135 0.2213 48.917
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] 4.769 -1.981 -2.788
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.958 r_dihedral_angle_3_deg 14.027 r_dihedral_angle_4_deg 12.971 r_dihedral_angle_1_deg 6.845 r_lrange_it 4.643 r_lrange_other 4.643 r_dihedral_angle_other_2_deg 3.456 r_scangle_it 2.951 r_scangle_other 2.95 r_mcangle_it 2.419
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.958 r_dihedral_angle_3_deg 14.027 r_dihedral_angle_4_deg 12.971 r_dihedral_angle_1_deg 6.845 r_lrange_it 4.643 r_lrange_other 4.643 r_dihedral_angle_other_2_deg 3.456 r_scangle_it 2.951 r_scangle_other 2.95 r_mcangle_it 2.419 r_mcangle_other 2.418 r_scbond_it 1.87 r_scbond_other 1.869 r_mcbond_it 1.547 r_mcbond_other 1.547 r_angle_refined_deg 1.477 r_angle_other_deg 1.283 r_symmetry_nbd_refined 0.24 r_nbd_refined 0.203 r_nbd_other 0.188 r_symmetry_nbd_other 0.172 r_nbtor_refined 0.157 r_xyhbond_nbd_refined 0.15 r_symmetry_nbtor_other 0.076 r_chiral_restr 0.071 r_symmetry_xyhbond_nbd_other 0.048 r_symmetry_xyhbond_nbd_refined 0.041 r_bond_refined_d 0.008 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 3089 Nucleic Acid Atoms Solvent Atoms 85 Heterogen Atoms 76
Software Software Software Name Purpose REFMAC refinement Coot model building DIALS data reduction PHASER phasing DIALS data scaling