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Human B4GALNT1 in Complex with UDP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 0.1 M Tris-BICINE, 30% w/v GOL_P4K (40% v/v Glycerol, 20% w/v PEG 4000), 0.2 M Sodium formate, 0.2 M Ammonium acetate, 0.2 M Sodium citrate tribasic dihydrate, 0.2 M Potassium sodium tartrate tetrahydrate, 0.2 M Sodium oxamate
Crystal Properties Matthews coefficient Solvent content 3.22 61.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.183 α = 90 b = 133.527 β = 94.83 c = 86.922 γ = 90
Symmetry Space Group P 1 21 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 EIGER2 X CdTe 9M 2024-02-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.6199 Diamond I24
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 2.67 66.76 99.3 0.127 0.15 0.079 0.989 8 6.8 38565
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) 2.67 2.79 94.2 1.107 1.363 0.784 0.477 1.1 5.6
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.674 66.76 38317 1897 99.023 0.193 0.1911 0.1911 0.2327 0.2328 79.968
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] 2.466 -0.642 0.389 -2.707
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.609 r_dihedral_angle_6_deg 14.397 r_lrange_it 13.401 r_dihedral_angle_2_deg 10.538 r_scangle_it 10.122 r_dihedral_angle_1_deg 6.956 r_mcangle_it 6.926 r_scbond_it 6.919 r_mcbond_it 4.686 r_angle_refined_deg 2.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.609 r_dihedral_angle_6_deg 14.397 r_lrange_it 13.401 r_dihedral_angle_2_deg 10.538 r_scangle_it 10.122 r_dihedral_angle_1_deg 6.956 r_mcangle_it 6.926 r_scbond_it 6.919 r_mcbond_it 4.686 r_angle_refined_deg 2.006 r_nbtor_refined 0.318 r_symmetry_nbd_refined 0.257 r_nbd_refined 0.213 r_symmetry_xyhbond_nbd_refined 0.141 r_chiral_restr 0.127 r_xyhbond_nbd_refined 0.126 r_ncsr_local_group_1 0.104 r_bond_refined_d 0.009 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7184 Nucleic Acid Atoms Solvent Atoms 27 Heterogen Atoms 138
Software Software Software Name Purpose REFMAC refinement DIALS data collection Aimless data scaling PHASER phasing ISOLDE model building Coot model building DIALS data reduction