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Structural and biochemical characterization of the N- acetylmannosamine-6-phosphate 2-epimerase from Clostridium perfringens
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4UTT PDB ENTRY 4UTT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 0.1 M PROPIONIC ACID, CACODYLATE, BIS-TRIS PROPANE BUFFER PH 8.0 AND 25% (W/V) PEG 1500
Crystal Properties Matthews coefficient Solvent content 2.36 47.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.714 α = 90 b = 82.147 β = 92.48 c = 75.195 γ = 90
Symmetry Space Group P 1 21 1
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 ADSC QUANTUM 315r M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.45 41.1 99.3 0.06 18 7 78204 4.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.45 1.53 95.8 0.46 4.3 5.9
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 PDB ENTRY 4UTT 1.45 42 76612 1565 99.21 0.14062 0.14004 0.1487 0.16915 0.1762 RANDOM 18.602
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] 0.42 0.49 -0.07 -0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.755 r_dihedral_angle_4_deg 21.166 r_dihedral_angle_3_deg 12.77 r_dihedral_angle_1_deg 5.415 r_scangle_it 3.559 r_scbond_it 2.524 r_angle_refined_deg 1.607 r_mcangle_it 1.346 r_mcbond_it 1.134 r_angle_other_deg 0.981
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.755 r_dihedral_angle_4_deg 21.166 r_dihedral_angle_3_deg 12.77 r_dihedral_angle_1_deg 5.415 r_scangle_it 3.559 r_scbond_it 2.524 r_angle_refined_deg 1.607 r_mcangle_it 1.346 r_mcbond_it 1.134 r_angle_other_deg 0.981 r_mcbond_other 0.273 r_nbd_refined 0.226 r_symmetry_vdw_other 0.225 r_nbd_other 0.202 r_symmetry_hbond_refined 0.177 r_nbtor_refined 0.176 r_xyhbond_nbd_refined 0.151 r_symmetry_vdw_refined 0.148 r_chiral_restr 0.097 r_nbtor_other 0.088 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_gen_planes_other 0.003 r_bond_other_d 0.002 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3502 Nucleic Acid Atoms Solvent Atoms 498 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement MOLREP phasing