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Human B4GALNT1 Apo Structure
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 3.32 63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.463 α = 90 b = 136.486 β = 96.076 c = 87.427 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 2.94 136.49 100 0.112 0.131 0.069 0.999 9.9 7.1 30064
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) 2.94 3.1 100 1.61 1.89 0.983 0.521 1.1 7.2
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 2.96 86.936 29240 1456 99.236 0.205 0.2019 0.2018 0.254 0.254 118.931
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] 1.023 1.464 -0.81 -0.514
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 16.317 r_dihedral_angle_3_deg 16.054 r_dihedral_angle_6_deg 14.786 r_scangle_it 12.206 r_dihedral_angle_2_deg 11.478 r_mcangle_it 10.447 r_scbond_it 8.378 r_dihedral_angle_1_deg 7.094 r_mcbond_it 6.953 r_angle_refined_deg 1.87
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 16.317 r_dihedral_angle_3_deg 16.054 r_dihedral_angle_6_deg 14.786 r_scangle_it 12.206 r_dihedral_angle_2_deg 11.478 r_mcangle_it 10.447 r_scbond_it 8.378 r_dihedral_angle_1_deg 7.094 r_mcbond_it 6.953 r_angle_refined_deg 1.87 r_symmetry_xyhbond_nbd_refined 0.653 r_nbtor_refined 0.309 r_symmetry_nbd_refined 0.25 r_nbd_refined 0.216 r_xyhbond_nbd_refined 0.136 r_chiral_restr 0.12 r_ncsr_local_group_1 0.105 r_bond_refined_d 0.007 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7015 Nucleic Acid Atoms Solvent Atoms 14 Heterogen Atoms 38
Software Software Software Name Purpose DIALS data collection DIALS data reduction Aimless data scaling PHASER phasing REFMAC refinement ISOLDE model building Coot model building