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Human B4GALNT1 in Complex with UDP-GalNac
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 3.23 61.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.1 α = 90 b = 134.922 β = 95.907 c = 86.584 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 2.75 54.66 99.5 0.186 0.219 0.114 0.992 6.2 7 35584
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) 2.75 2.88 96.3 1.442 1.742 0.964 0.389 1 6.3
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 2.75 54.656 35558 1761 99.602 0.19 0.1887 0.1887 0.2248 0.2248 75.617
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] 0.834 -0.836 -0.845 0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.28 r_dihedral_angle_6_deg 14.932 r_lrange_it 13.35 r_dihedral_angle_2_deg 10.629 r_scangle_it 9.529 r_mcangle_it 7.115 r_dihedral_angle_1_deg 6.838 r_scbond_it 6.331 r_mcbond_it 4.606 r_angle_refined_deg 1.884
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.28 r_dihedral_angle_6_deg 14.932 r_lrange_it 13.35 r_dihedral_angle_2_deg 10.629 r_scangle_it 9.529 r_mcangle_it 7.115 r_dihedral_angle_1_deg 6.838 r_scbond_it 6.331 r_mcbond_it 4.606 r_angle_refined_deg 1.884 r_symmetry_xyhbond_nbd_refined 0.323 r_nbtor_refined 0.309 r_symmetry_nbd_refined 0.296 r_nbd_refined 0.206 r_xyhbond_nbd_refined 0.146 r_chiral_restr 0.123 r_ncsr_local_group_1 0.091 r_bond_refined_d 0.008 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7316 Nucleic Acid Atoms Solvent Atoms 74 Heterogen Atoms 200
Software Software Software Name Purpose REFMAC refinement DIALS data collection Aimless data scaling PHASER phasing ISOLDE model building Coot model building DIALS data reduction