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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, HANGING DROP 291 1.26M Sodium phosphate monobasic monohydrate,
0.14M Potassium phosphate dibasic
Crystal Properties Matthews coefficient Solvent content 2.31 46.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.6 α = 90 b = 92.81 β = 90 c = 71.32 γ = 90
Symmetry Space Group P 21 21 2
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 2022-12-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.97851 SSRF BL19U1
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 1.73 46.71 100 0.993 11.7 12.9 57948
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 1.73 1.76 0.804
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 1.73 46.71 54915 2986 99.97 0.20212 0.20042 0.2083 0.23359 0.2389 RANDOM 34.59
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] 1.04 -0.71 -0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.068 r_dihedral_angle_4_deg 15.837 r_dihedral_angle_3_deg 13.257 r_long_range_B_refined 7.146 r_long_range_B_other 7.099 r_dihedral_angle_1_deg 5.969 r_scangle_other 4.99 r_mcangle_it 3.844 r_mcangle_other 3.844 r_scbond_it 3.083
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.068 r_dihedral_angle_4_deg 15.837 r_dihedral_angle_3_deg 13.257 r_long_range_B_refined 7.146 r_long_range_B_other 7.099 r_dihedral_angle_1_deg 5.969 r_scangle_other 4.99 r_mcangle_it 3.844 r_mcangle_other 3.844 r_scbond_it 3.083 r_scbond_other 3.083 r_mcbond_it 2.473 r_mcbond_other 2.468 r_angle_refined_deg 1.446 r_angle_other_deg 0.785 r_chiral_restr 0.088 r_bond_refined_d 0.011 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 3464 Nucleic Acid Atoms Solvent Atoms 184 Heterogen Atoms 67
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing