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X-ray structure of a glucosamine N-Acetyltransferase from Clostridium acetobutylicum in complex with galactosamine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5KF1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 7-10% PEG-5000, 100 mM HEPPS, 20 mM galactosamine
Crystal Properties Matthews coefficient Solvent content 2.17 43.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.076 α = 90 b = 43.84 β = 120.81 c = 74.169 γ = 90
Symmetry Space Group C 1 2 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 Bruker Platinum 135 2015-12-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 50 97.9 0.072 0.072 11.6 4.4 25686
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 93.6 0.302 2.4 2.5
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 5KF1 1.9 50 24410 1275 97.9 0.17 0.167 0.1795 0.215 0.2293 RANDOM 22.83
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] 0.09 -0.52 2.06 -0.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.577 r_dihedral_angle_3_deg 16.064 r_dihedral_angle_4_deg 12.626 r_dihedral_angle_1_deg 7.412 r_long_range_B_refined 6.769 r_long_range_B_other 6.769 r_scangle_other 5.257 r_mcangle_it 3.552 r_mcangle_other 3.551 r_scbond_it 3.482
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.577 r_dihedral_angle_3_deg 16.064 r_dihedral_angle_4_deg 12.626 r_dihedral_angle_1_deg 7.412 r_long_range_B_refined 6.769 r_long_range_B_other 6.769 r_scangle_other 5.257 r_mcangle_it 3.552 r_mcangle_other 3.551 r_scbond_it 3.482 r_scbond_other 3.481 r_mcbond_it 2.422 r_mcbond_other 2.419 r_angle_refined_deg 1.847 r_angle_other_deg 0.859 r_chiral_restr 0.278 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 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 2615 Nucleic Acid Atoms Solvent Atoms 177 Heterogen Atoms 114
Software Software Software Name Purpose REFMAC refinement SAINT data reduction SADABS data scaling PHASER phasing