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Crystal structure of Campylobacter jejuni 5'-methylthioadenosine/S-adenosyl homocysteine nucleosidase (MTAN) complexed with 5'-deoxy-5'-Propyl-DADMe-Immucillin-A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4WKN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 295 100 mM Bis-Tris pH 6.5, 25% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.1 40.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.357 α = 90 b = 90.082 β = 105.51 c = 67.374 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 RAYONIX MX-225 2017-03-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.97931 APS 31-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.67 64.92 99.7 0.99 11.6 7.5 49714
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.67 1.7 97.5 0.73 2 6.6
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 4WKN 1.67 64.92 47130 2549 99.68 0.1808 0.17973 0.1905 0.20053 0.2055 RANDOM 20.811
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] 0.37 -0.47 0.27 -0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.657 r_dihedral_angle_4_deg 20.945 r_dihedral_angle_3_deg 12.799 r_dihedral_angle_1_deg 6.041 r_long_range_B_refined 3.752 r_long_range_B_other 3.752 r_scangle_other 1.769 r_mcangle_it 1.502 r_mcangle_other 1.501 r_angle_refined_deg 1.317
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.657 r_dihedral_angle_4_deg 20.945 r_dihedral_angle_3_deg 12.799 r_dihedral_angle_1_deg 6.041 r_long_range_B_refined 3.752 r_long_range_B_other 3.752 r_scangle_other 1.769 r_mcangle_it 1.502 r_mcangle_other 1.501 r_angle_refined_deg 1.317 r_scbond_it 1.054 r_scbond_other 1.054 r_angle_other_deg 0.871 r_mcbond_it 0.853 r_mcbond_other 0.853 r_chiral_restr 0.175 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.002 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 3532 Nucleic Acid Atoms Solvent Atoms 349 Heterogen Atoms 70
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing