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Amuc0121_S1_15 in complex with D-Galactose
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 298 Morpheus H12-
37.5 % Precipitant mix 4 (25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350),
0.1 M Buffer system 3 pH 8.5 (Tris (base); BICINE),
0.1 M amino acids (0.2M DL-Glutamic acid monohydrate; 0.2M DL-Alanine; 0.2M Glycine; 0.2M DL-Lysine monohydrochloride; 0.2M DL-Serine)
36 mg/ml Amuc0121 with 100 mM D-Galactose
Crystal Properties Matthews coefficient Solvent content 2.3 46.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.51 α = 90 b = 91.49 β = 90 c = 162.08 γ = 90
Symmetry Space Group P 21 21 21
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 S 16M 2021-09-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 1.0 Diamond I04
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 1.56 61.607 100 0.999 15.8 6.5 141184
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 1.56 1.59 0.589
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 1.56 61.607 141085 7026 99.975 0.14 0.1379 0.137 0.1843 0.1844 30.965
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] -1.064 1.906 -0.843
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.934 r_lrange_it 15.56 r_lrange_other 15.121 r_dihedral_angle_3_deg 13.191 r_scangle_it 12.455 r_scangle_other 12.454 r_mcangle_other 9.008 r_mcangle_it 9.006 r_scbond_it 8.826 r_scbond_other 8.825
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.934 r_lrange_it 15.56 r_lrange_other 15.121 r_dihedral_angle_3_deg 13.191 r_scangle_it 12.455 r_scangle_other 12.454 r_mcangle_other 9.008 r_mcangle_it 9.006 r_scbond_it 8.826 r_scbond_other 8.825 r_dihedral_angle_2_deg 6.7 r_dihedral_angle_1_deg 6.612 r_mcbond_it 6.597 r_mcbond_other 6.593 r_rigid_bond_restr 3.6 r_angle_refined_deg 1.648 r_angle_other_deg 0.581 r_nbd_other 0.237 r_nbd_refined 0.215 r_symmetry_nbd_other 0.199 r_symmetry_xyhbond_nbd_refined 0.182 r_nbtor_refined 0.175 r_xyhbond_nbd_refined 0.132 r_metal_ion_refined 0.104 r_symmetry_xyhbond_nbd_other 0.102 r_chiral_restr 0.084 r_symmetry_nbtor_other 0.083 r_symmetry_nbd_refined 0.07 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7525 Nucleic Acid Atoms Solvent Atoms 596 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing