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Crystal structure of AaNGT complexed to UDP-Gal
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3Q3E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291 magnesium chloride, HEPES, PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.46 50.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.338 α = 90 b = 113.331 β = 90 c = 260.115 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 PILATUS3 S 6M 2019-12-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.9793 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.76 20 99.9 0.065 0.999 14.2 7.7 139852
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.76 1.86 1.796 0.43
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.76 20 134160 5578 99.88 0.17568 0.17434 0.1837 0.20714 0.2125 RANDOM 37.743
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] 0.29 0.12 -0.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 20.832 r_dihedral_angle_3_deg 15.862 r_long_range_B_refined 7.21 r_long_range_B_other 7.182 r_dihedral_angle_1_deg 6.23 r_scangle_other 5.94 r_scbond_it 4.033 r_scbond_other 4.033 r_mcangle_it 3.532 r_mcangle_other 3.532
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 20.832 r_dihedral_angle_3_deg 15.862 r_long_range_B_refined 7.21 r_long_range_B_other 7.182 r_dihedral_angle_1_deg 6.23 r_scangle_other 5.94 r_scbond_it 4.033 r_scbond_other 4.033 r_mcangle_it 3.532 r_mcangle_other 3.532 r_mcbond_it 2.666 r_mcbond_other 2.661 r_angle_refined_deg 1.466 r_angle_other_deg 0.489 r_chiral_restr 0.075 r_gen_planes_refined 0.009 r_bond_refined_d 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10134 Nucleic Acid Atoms Solvent Atoms 781 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing