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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 monobasic
Crystal Properties Matthews coefficient Solvent content 2.29 46.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.84 α = 90 b = 87.84 β = 90 c = 140.24 γ = 90
Symmetry Space Group P 42 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 PILATUS3 2M 2021-12-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17B1 0.97628 SSRF BL17B1
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 2.41 46.75 100 0.999 13.8 25.7 21910
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 2.41 2.5 0.786
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 2.41 46.54 20838 1070 99.95 0.21057 0.2083 0.2115 0.25261 0.2534 RANDOM 41.343
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] -0.32 -0.32 0.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.6 r_dihedral_angle_4_deg 18.613 r_dihedral_angle_3_deg 14.45 r_long_range_B_other 7.48 r_long_range_B_refined 7.475 r_dihedral_angle_1_deg 7.321 r_scangle_other 4.829 r_mcangle_it 4.569 r_mcangle_other 4.568 r_scbond_it 2.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.6 r_dihedral_angle_4_deg 18.613 r_dihedral_angle_3_deg 14.45 r_long_range_B_other 7.48 r_long_range_B_refined 7.475 r_dihedral_angle_1_deg 7.321 r_scangle_other 4.829 r_mcangle_it 4.569 r_mcangle_other 4.568 r_scbond_it 2.84 r_scbond_other 2.839 r_mcbond_it 2.802 r_mcbond_other 2.801 r_angle_refined_deg 1.329 r_angle_other_deg 1.157 r_chiral_restr 0.057 r_bond_refined_d 0.005 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 3466 Nucleic Acid Atoms Solvent Atoms 84 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling Coot model building PHASER phasing