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a mutant of glycosyktransferase in complex with UDP and Reb D
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 pH6.5
Crystal Properties Matthews coefficient Solvent content 2.52 51.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.444 α = 90 b = 83.496 β = 90 c = 110.645 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 2020-06-26 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 2.34 36.88 100 0.06 0.977 15.8 6 21963
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 2.34 2.38 0.22 0.983
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 2.34 35.215 21919 1076 99.786 0.199 0.1963 0.2074 0.243 0.2427 58.905
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] 5.819 -2.024 -3.795
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.113 r_dihedral_angle_3_deg 12.995 r_dihedral_angle_4_deg 10.566 r_lrange_other 7.861 r_lrange_it 7.857 r_scangle_it 6.653 r_scangle_other 6.651 r_dihedral_angle_1_deg 6.503 r_mcangle_it 5.034 r_mcangle_other 5.032
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.113 r_dihedral_angle_3_deg 12.995 r_dihedral_angle_4_deg 10.566 r_lrange_other 7.861 r_lrange_it 7.857 r_scangle_it 6.653 r_scangle_other 6.651 r_dihedral_angle_1_deg 6.503 r_mcangle_it 5.034 r_mcangle_other 5.032 r_scbond_it 4.639 r_scbond_other 4.638 r_mcbond_it 3.629 r_mcbond_other 3.623 r_dihedral_angle_other_2_deg 1.739 r_angle_refined_deg 1.277 r_angle_other_deg 1.12 r_nbd_refined 0.189 r_symmetry_nbd_other 0.172 r_symmetry_nbd_refined 0.164 r_nbd_other 0.151 r_nbtor_refined 0.15 r_symmetry_xyhbond_nbd_refined 0.12 r_xyhbond_nbd_refined 0.106 r_symmetry_nbtor_other 0.074 r_chiral_restr 0.048 r_gen_planes_refined 0.004 r_bond_refined_d 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3088 Nucleic Acid Atoms Solvent Atoms 30 Heterogen Atoms 103
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Coot model building PHASER phasing DIALS data scaling