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Amuc1755_S1_16 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 1.6 M Sodium Malonate
Amuc1755 2,75 mg/ml with 100 mM D-Galactose
Crystal Properties Matthews coefficient Solvent content 2.49 50.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 143.08 α = 90 b = 143.08 β = 90 c = 50.41 γ = 120
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 2021-09-14 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 2.1 71.54 100 0.999 15.8 9.9 344730
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 2.1 2.16 0.666
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 2.1 71.54 34729 1753 99.994 0.168 0.1662 0.1762 0.2072 0.2118 37.145
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] -0.55 -0.275 -0.55 1.785
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.664 r_dihedral_angle_6_deg 15.6 r_dihedral_angle_2_deg 9.772 r_lrange_other 7.314 r_lrange_it 7.31 r_dihedral_angle_1_deg 7.15 r_scangle_it 6.264 r_scangle_other 6.263 r_scbond_it 4.059 r_scbond_other 4.059
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.664 r_dihedral_angle_6_deg 15.6 r_dihedral_angle_2_deg 9.772 r_lrange_other 7.314 r_lrange_it 7.31 r_dihedral_angle_1_deg 7.15 r_scangle_it 6.264 r_scangle_other 6.263 r_scbond_it 4.059 r_scbond_other 4.059 r_mcangle_it 3.901 r_mcangle_other 3.901 r_mcbond_it 2.757 r_mcbond_other 2.757 r_angle_refined_deg 1.732 r_angle_other_deg 0.589 r_nbd_refined 0.213 r_nbd_other 0.21 r_symmetry_nbd_other 0.196 r_nbtor_refined 0.179 r_xyhbond_nbd_refined 0.154 r_metal_ion_refined 0.136 r_symmetry_xyhbond_nbd_refined 0.114 r_symmetry_nbtor_other 0.087 r_chiral_restr 0.082 r_symmetry_nbd_refined 0.071 r_bond_refined_d 0.007 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 4214 Nucleic Acid Atoms Solvent Atoms 116 Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing