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beta-1,4-galacosyltransferase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8XC8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 0.2M Magnesium acetate tetrahydrate,
0.1M Sodium cacodylate trihydrate,
20% PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.28 46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 136.148 α = 90 b = 57.26 β = 116.49 c = 77.18 γ = 90
Symmetry Space Group C 1 2 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 PILATUS3 S 6M 2023-10-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.97853 SSRF BL18U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.87 45.88 99.8 0.995 9.8 3.4 44062
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.87 1.91 0.819
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 (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 1.87 45.88 41869 2191 99.69 0.21024 0.20838 0.2246 0.24687 0.2615 RANDOM 36.636
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] -0.8 -1.37 6.61 -2.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.779 r_dihedral_angle_4_deg 20.255 r_dihedral_angle_3_deg 14.142 r_long_range_B_refined 6.151 r_long_range_B_other 6.135 r_dihedral_angle_1_deg 5.926 r_scangle_other 4.366 r_mcangle_it 3.271 r_mcangle_other 3.271 r_scbond_it 2.653
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.779 r_dihedral_angle_4_deg 20.255 r_dihedral_angle_3_deg 14.142 r_long_range_B_refined 6.151 r_long_range_B_other 6.135 r_dihedral_angle_1_deg 5.926 r_scangle_other 4.366 r_mcangle_it 3.271 r_mcangle_other 3.271 r_scbond_it 2.653 r_scbond_other 2.653 r_mcbond_it 2.092 r_mcbond_other 2.09 r_angle_refined_deg 1.427 r_angle_other_deg 0.792 r_chiral_restr 0.086 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3518 Nucleic Acid Atoms Solvent Atoms 108 Heterogen Atoms 74
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling Coot model building PHASER phasing