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Amuc0953_S1_20 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 20 % PEG 3350
0.2 M Sodium Iodide
55 mg/ml Amuc0953 with 100 mM D-Galactose
Crystal Properties Matthews coefficient Solvent content 3.59 65.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 187.28 α = 90 b = 187.28 β = 90 c = 221.77 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 2022-01-31 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 2.9 78.476 100 0.998 9.9 6.5 1156298
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 2.9 2.95 0.641
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 2.9 78.476 84299 4384 99.956 0.214 0.2118 0.2095 0.2566 0.2511 90.956
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] -2.084 -2.084 4.169
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.136 r_dihedral_angle_6_deg 14.467 r_lrange_it 13.935 r_lrange_other 13.935 r_dihedral_angle_2_deg 10.994 r_scangle_it 10.223 r_scangle_other 10.222 r_mcangle_it 8.407 r_mcangle_other 8.407 r_dihedral_angle_1_deg 7.726
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.136 r_dihedral_angle_6_deg 14.467 r_lrange_it 13.935 r_lrange_other 13.935 r_dihedral_angle_2_deg 10.994 r_scangle_it 10.223 r_scangle_other 10.222 r_mcangle_it 8.407 r_mcangle_other 8.407 r_dihedral_angle_1_deg 7.726 r_scbond_it 6.776 r_scbond_other 6.776 r_mcbond_it 5.666 r_mcbond_other 5.666 r_angle_refined_deg 1.558 r_angle_other_deg 0.538 r_metal_ion_refined 0.502 r_symmetry_xyhbond_nbd_refined 0.268 r_nbd_refined 0.234 r_symmetry_nbd_other 0.211 r_nbtor_refined 0.182 r_symmetry_nbd_refined 0.18 r_nbd_other 0.176 r_xyhbond_nbd_refined 0.147 r_symmetry_nbtor_other 0.085 r_ncsr_local_group_1 0.072 r_chiral_restr 0.07 r_symmetry_xyhbond_nbd_other 0.01 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19044 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing