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Crystal structure of AaNGT complexed to UDP and a peptide
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 7 291 polyacrylic acid 5,100 sodium salt, HEPES sodium salt
Crystal Properties Matthews coefficient Solvent content 2.35 47.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.025 α = 90 b = 111.477 β = 90 c = 256.37 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 2019-07-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9762 Diamond I03
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 2.8 20 99.7 0.177 0.996 8.2 8.4 34243
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 2.8 2.95 0.352
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 2.8 19.96 32753 1344 99.39 0.18091 0.1785 0.181 0.23722 0.2333 RANDOM 81.251
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] -2.45 5.32 -2.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.403 r_dihedral_angle_4_deg 22.098 r_dihedral_angle_3_deg 19.396 r_long_range_B_refined 8.855 r_long_range_B_other 8.854 r_dihedral_angle_1_deg 7.58 r_scangle_other 6.425 r_mcangle_it 5.986 r_mcangle_other 5.986 r_scbond_it 4.094
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.403 r_dihedral_angle_4_deg 22.098 r_dihedral_angle_3_deg 19.396 r_long_range_B_refined 8.855 r_long_range_B_other 8.854 r_dihedral_angle_1_deg 7.58 r_scangle_other 6.425 r_mcangle_it 5.986 r_mcangle_other 5.986 r_scbond_it 4.094 r_scbond_other 4.094 r_mcbond_it 3.894 r_mcbond_other 3.891 r_angle_refined_deg 1.656 r_angle_other_deg 1.287 r_chiral_restr 0.072 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 9998 Nucleic Acid Atoms Solvent Atoms 5 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing