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Structure of Epimerase Mth373 bound to uridine-5'-diphosphate-xylopyranose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8W3U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 294 0.1 M sodium citrate tribasic dihydrate, 18% w/v PEG 3,350
Crystal Properties Matthews coefficient Solvent content 2.6 52.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 139.327 α = 90 b = 139.327 β = 90 c = 226.946 γ = 120
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 2017-12-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.95368 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.96 44.75 98.6 0.162 0.167 0.037 0.996 16.3 19.9 59615
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.96 2.01 80.6 0.615 0.633 0.145 0.951 17.6
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 1.97 44.75 56236 2945 98.11 0.17233 0.17064 0.1828 0.20416 0.2131 RANDOM 25.984
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] 1.32 0.66 1.32 -4.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.205 r_dihedral_angle_4_deg 20.889 r_dihedral_angle_3_deg 13.493 r_dihedral_angle_1_deg 7.257 r_long_range_B_refined 5.406 r_long_range_B_other 5.405 r_scangle_other 3.919 r_mcangle_it 3.263 r_mcangle_other 3.263 r_scbond_it 2.747
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.205 r_dihedral_angle_4_deg 20.889 r_dihedral_angle_3_deg 13.493 r_dihedral_angle_1_deg 7.257 r_long_range_B_refined 5.406 r_long_range_B_other 5.405 r_scangle_other 3.919 r_mcangle_it 3.263 r_mcangle_other 3.263 r_scbond_it 2.747 r_scbond_other 2.747 r_mcbond_it 2.33 r_mcbond_other 2.327 r_angle_refined_deg 1.597 r_angle_other_deg 1.41 r_chiral_restr 0.086 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 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 5143 Nucleic Acid Atoms Solvent Atoms 474 Heterogen Atoms 173
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction MOLREP phasing