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The crystal structure of Non-hydrolyzing UDPGlcNAc 2-epimerase in complex with UDP-glucose
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 5.5 293 0.2M lithium sulfate, 0.1M Bis tris pH 5.5, 25% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.39 48.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.833 α = 74.867 b = 104.941 β = 72.918 c = 106.84 γ = 68.076
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 2019-12-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE TPS 05A 1 NSRRC TPS 05A
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 2.09 21.56 95.2 0.057 19.7 2.2 176474
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 2.1 2.18 0.057
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 2.092 21.558 176474 8824 95.09 0.202 0.2008 0.2044 0.2278 0.2278 28.96
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] 0.119 0.018 0.108 0.052 0.02 -0.096
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.758 r_dihedral_angle_4_deg 15.456 r_dihedral_angle_3_deg 15.3 r_lrange_it 7.12 r_lrange_other 7.077 r_dihedral_angle_1_deg 6.585 r_scangle_it 5.225 r_scangle_other 5.225 r_mcangle_other 3.75 r_mcangle_it 3.749
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.758 r_dihedral_angle_4_deg 15.456 r_dihedral_angle_3_deg 15.3 r_lrange_it 7.12 r_lrange_other 7.077 r_dihedral_angle_1_deg 6.585 r_scangle_it 5.225 r_scangle_other 5.225 r_mcangle_other 3.75 r_mcangle_it 3.749 r_scbond_it 3.305 r_scbond_other 3.305 r_mcbond_it 2.532 r_mcbond_other 2.53 r_angle_other_deg 1.558 r_angle_refined_deg 1.495 r_symmetry_nbd_refined 0.211 r_nbd_other 0.209 r_nbd_refined 0.203 r_symmetry_nbd_other 0.2 r_xyhbond_nbd_refined 0.181 r_metal_ion_refined 0.168 r_symmetry_xyhbond_nbd_refined 0.167 r_nbtor_refined 0.148 r_ncsr_local_group_13 0.09 r_ncsr_local_group_8 0.088 r_ncsr_local_group_11 0.088 r_ncsr_local_group_22 0.087 r_ncsr_local_group_9 0.086 r_ncsr_local_group_20 0.086 r_ncsr_local_group_18 0.085 r_ncsr_local_group_7 0.084 r_ncsr_local_group_1 0.083 r_ncsr_local_group_10 0.083 r_ncsr_local_group_12 0.081 r_ncsr_local_group_28 0.081 r_ncsr_local_group_14 0.08 r_ncsr_local_group_5 0.079 r_ncsr_local_group_19 0.078 r_ncsr_local_group_25 0.078 r_ncsr_local_group_27 0.077 r_ncsr_local_group_3 0.076 r_chiral_restr 0.074 r_ncsr_local_group_21 0.074 r_ncsr_local_group_15 0.073 r_ncsr_local_group_23 0.073 r_ncsr_local_group_2 0.072 r_ncsr_local_group_16 0.072 r_ncsr_local_group_24 0.072 r_ncsr_local_group_17 0.071 r_symmetry_xyhbond_nbd_other 0.07 r_ncsr_local_group_26 0.069 r_ncsr_local_group_4 0.068 r_ncsr_local_group_6 0.068 r_symmetry_nbtor_other 0.067 r_bond_other_d 0.018 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_gen_planes_other 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 22403 Nucleic Acid Atoms Solvent Atoms 1499 Heterogen Atoms 295
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing