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The crystal structure of Non-hydrolyzing UDPGlcNAc 2-epimerase in complex with UDP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VGV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.2M lithium sulfate, 0.1M Bis tris pH5.5, 25% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.36 47.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.82 α = 74.536 b = 104.77 β = 73.051 c = 106.314 γ = 68.39
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RAYONIX MX300HE 2020-04-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL15A1 1 NSRRC BL15A1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) 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 2.58 19.895 94.1 0.05 23.8 2.4 91395
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.68 0.05
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT NONE 1VGV 2.58 19.895 91395 4644 93.946 0.212 0.2098 0.2108 0.2488 0.2416 45.239
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] 0.417 -0.312 0.101 -0.371 0.044 -0.098
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.582 r_dihedral_angle_4_deg 17.649 r_dihedral_angle_3_deg 16.815 r_lrange_other 8.4 r_lrange_it 8.399 r_dihedral_angle_1_deg 6.468 r_scangle_it 5.845 r_scangle_other 5.844 r_mcangle_it 5.185 r_mcangle_other 5.185
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.582 r_dihedral_angle_4_deg 17.649 r_dihedral_angle_3_deg 16.815 r_lrange_other 8.4 r_lrange_it 8.399 r_dihedral_angle_1_deg 6.468 r_scangle_it 5.845 r_scangle_other 5.844 r_mcangle_it 5.185 r_mcangle_other 5.185 r_scbond_it 3.624 r_scbond_other 3.624 r_mcbond_it 3.362 r_mcbond_other 3.362 r_angle_refined_deg 1.454 r_angle_other_deg 1.18 r_nbd_other 0.215 r_nbd_refined 0.195 r_symmetry_nbd_other 0.183 r_xyhbond_nbd_refined 0.175 r_symmetry_nbd_refined 0.166 r_symmetry_xyhbond_nbd_refined 0.165 r_nbtor_refined 0.146 r_symmetry_nbtor_other 0.077 r_ncsr_local_group_28 0.076 r_ncsr_local_group_18 0.074 r_ncsr_local_group_24 0.074 r_ncsr_local_group_6 0.071 r_ncsr_local_group_22 0.071 r_ncsr_local_group_17 0.07 r_ncsr_local_group_14 0.068 r_ncsr_local_group_15 0.068 r_ncsr_local_group_19 0.068 r_ncsr_local_group_26 0.068 r_ncsr_local_group_27 0.068 r_ncsr_local_group_2 0.067 r_ncsr_local_group_12 0.067 r_ncsr_local_group_13 0.067 r_ncsr_local_group_7 0.066 r_ncsr_local_group_25 0.066 r_ncsr_local_group_9 0.065 r_ncsr_local_group_10 0.065 r_symmetry_xyhbond_nbd_other 0.064 r_ncsr_local_group_4 0.064 r_ncsr_local_group_23 0.064 r_ncsr_local_group_5 0.063 r_ncsr_local_group_11 0.063 r_ncsr_local_group_16 0.063 r_chiral_restr 0.061 r_ncsr_local_group_1 0.061 r_ncsr_local_group_21 0.06 r_ncsr_local_group_8 0.058 r_ncsr_local_group_3 0.057 r_ncsr_local_group_20 0.057 r_metal_ion_refined 0.012 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 22203 Nucleic Acid Atoms Solvent Atoms 334 Heterogen Atoms 208
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing