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Crystal Structure of UDP-Glucuronic acid 4-epimerase Y149F mutant from Bacillus cereus in complex with UDP-4-DEOXY-4-FLUORO-Glucuronic acid and NAD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5U4Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8 293 200 mM potassium acetate, 14-24% PEG3350, 2 mM NAD, 2 mM UDP-4-FLUORO-4-DEOXY-Glucuronic acid
Crystal Properties Matthews coefficient Solvent content 1.98 37.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.199 α = 97.25 b = 58.222 β = 98.18 c = 64.439 γ = 109.93
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 EIGER X 16M 2019-03-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.98 SLS X06SA
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 1.7 45.25 93 0.99 8.4 9.1 54213
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 1.7 1.74 0.69
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 5U4Q 1.7 45.25 54213 2808 92.42 0.1746 0.1725 0.1827 0.2154 0.222 RANDOM 29.357
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] -1.38 -0.8 -1 -0.86 0.92 2.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.321 r_dihedral_angle_4_deg 14.68 r_dihedral_angle_3_deg 14.587 r_dihedral_angle_1_deg 6.781 r_angle_refined_deg 1.599 r_angle_other_deg 1.38 r_chiral_restr 0.082 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.321 r_dihedral_angle_4_deg 14.68 r_dihedral_angle_3_deg 14.587 r_dihedral_angle_1_deg 6.781 r_angle_refined_deg 1.599 r_angle_other_deg 1.38 r_chiral_restr 0.082 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4930 Nucleic Acid Atoms Solvent Atoms 168 Heterogen Atoms 162
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling MOLREP phasing