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Amuc1074_S1_11 in complex with N-acetyl D-glucosamine
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 E9:
30 % Precipitant mix 1 (40% v/v PEG 500* MME; 20 % w/v PEG 20000)
0.1 M Buffer system 3 pH 8.5 (Tris (base); BICINE)
0.12 M Ethylene glycols (0.3M Diethylene glycol; 0.3M Triethylene glycol; 0.3M Tetraethylene glycol; 0.3M Pentaethylene glycol)
20 mg/ml Amuc1074 with 100 mM N-acetyl D-glucosamine
Crystal Properties Matthews coefficient Solvent content 3.04 59.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.01 α = 90 b = 130.01 β = 90 c = 86.27 γ = 90
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 2021-07-14 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 1.38 71.88 100 0.998 10.7 6.5 146947
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 1.38 1.4 0.707
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 1.38 41.147 146929 7209 99.963 0.168 0.1673 0.1731 0.1841 0.1902 23.564
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] -1.328 -1.328 2.655
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.281 r_dihedral_angle_3_deg 12.709 r_dihedral_angle_1_deg 7.021 r_dihedral_angle_2_deg 6.74 r_lrange_it 5.461 r_lrange_other 5.414 r_scangle_it 4.635 r_scangle_other 4.634 r_scbond_it 3.073 r_scbond_other 3.072
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.281 r_dihedral_angle_3_deg 12.709 r_dihedral_angle_1_deg 7.021 r_dihedral_angle_2_deg 6.74 r_lrange_it 5.461 r_lrange_other 5.414 r_scangle_it 4.635 r_scangle_other 4.634 r_scbond_it 3.073 r_scbond_other 3.072 r_mcangle_it 2.452 r_mcangle_other 2.452 r_angle_refined_deg 1.898 r_mcbond_it 1.741 r_mcbond_other 1.741 r_angle_other_deg 0.675 r_nbd_refined 0.225 r_nbd_other 0.19 r_symmetry_nbd_other 0.184 r_nbtor_refined 0.182 r_metal_ion_refined 0.144 r_xyhbond_nbd_refined 0.125 r_symmetry_nbd_refined 0.104 r_chiral_restr 0.103 r_symmetry_xyhbond_nbd_refined 0.099 r_symmetry_nbtor_other 0.08 r_bond_refined_d 0.011 r_gen_planes_refined 0.011 r_symmetry_xyhbond_nbd_other 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4218 Nucleic Acid Atoms Solvent Atoms 437 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing