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Crystal structure of Pcryo_0616, the aminotransferase required to synthesize UDP-N-acetyl-3-amino-D-glucosaminuronic acid (UDP-GlcNAc3NA)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NYU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 Protein incubated with 5 mM UDP and 1 mM PLP. Precipitant: 18 - 22% poly(ethylene glycol) 8000, 200 mM LiCl, and 100 mM HEPPS (pH 8.0)
Crystal Properties Matthews coefficient Solvent content 2.3 46.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.828 α = 90 b = 96.344 β = 90 c = 139.658 γ = 90
Symmetry Space Group C 2 2 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 Bruker PHOTON II 2019-03-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE BRUKER D8 QUEST 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 1.25 50 97.8 0.051 19.5 7.8 106460
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.25 1.35 91.4 0.42 2.7 3.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 3nyu 1.25 28.93 101098 5362 97.78 0.1548 0.154 0.1539 0.1704 0.1702 RANDOM 10.402
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] 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.399 r_dihedral_angle_4_deg 24.21 r_dihedral_angle_3_deg 11.465 r_dihedral_angle_1_deg 6.249 r_angle_refined_deg 1.776 r_angle_other_deg 1.58 r_chiral_restr 0.243 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_gen_planes_other 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.399 r_dihedral_angle_4_deg 24.21 r_dihedral_angle_3_deg 11.465 r_dihedral_angle_1_deg 6.249 r_angle_refined_deg 1.776 r_angle_other_deg 1.58 r_chiral_restr 0.243 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_gen_planes_other 0.001 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2791 Nucleic Acid Atoms Solvent Atoms 692 Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction SAINT data reduction SADABS data scaling PHASER phasing