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Structural characterisation of NanE, ManNac6P C2 epimerase, from Clostridium perfingens
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 NA CACODYLATE PH 6.5, 0.2 M CA ACETATE, 24.5% (W/V) PEG 2K MME AND 5% (V/V) PEG 400
Crystal Properties Matthews coefficient Solvent content 2.37 48.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.756 α = 89.9 b = 75.584 β = 89.91 c = 82.173 γ = 92.92
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 210 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 1.9 41.1 91 0.08 10 1.9 63357
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 1.9 2 85.9 0.42 1.5 1.8
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 1.9 50 60227 3129 90.98 0.18832 0.18515 0.1934 0.24805 0.2177 RANDOM 29.033
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] 0.97 0.44 0.23 -0.47 -0.03 -0.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.267 r_dihedral_angle_4_deg 21.505 r_dihedral_angle_3_deg 15.619 r_dihedral_angle_1_deg 5.806 r_scangle_it 2.896 r_scbond_it 1.94 r_angle_refined_deg 1.622 r_mcangle_it 1.076 r_angle_other_deg 1.005 r_mcbond_it 0.681
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.267 r_dihedral_angle_4_deg 21.505 r_dihedral_angle_3_deg 15.619 r_dihedral_angle_1_deg 5.806 r_scangle_it 2.896 r_scbond_it 1.94 r_angle_refined_deg 1.622 r_mcangle_it 1.076 r_angle_other_deg 1.005 r_mcbond_it 0.681 r_mcbond_other 0.242 r_chiral_restr 0.099 r_bond_refined_d 0.017 r_gen_planes_refined 0.006 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_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 7028 Nucleic Acid Atoms Solvent Atoms 999 Heterogen Atoms 80
Software Software Software Name Purpose REFMAC refinement MOLREP phasing