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Crystal structure of Campylobacter jejuni 5'-methylthioadenosine/S-adenosyl homocysteine nucleosidase (MTAN) complexed with butylthio-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 8.5 295 100 mM Tris pH 8.5, 800 mM Lithium Chloride, 32% (w/v) PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.2 43.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.156 α = 90 b = 91.407 β = 109.97 c = 78.431 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 1.95 73.72 99.4 0.99 11.5 4.1 65501
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 1.95 2 99.9 0.66 1.9 4.1
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4WKN 1.95 73.72 62193 3289 99.39 0.22497 0.22347 0.2534 0.2398 RANDOM 43.19
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] -0.5 2.34 -2.9 1.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.243 r_dihedral_angle_4_deg 20.385 r_dihedral_angle_3_deg 15.968 r_dihedral_angle_1_deg 6.316 r_long_range_B_other 4.938 r_long_range_B_refined 4.937 r_scangle_other 3.356 r_mcangle_it 3.031 r_mcangle_other 3.031 r_scbond_it 2.083
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.243 r_dihedral_angle_4_deg 20.385 r_dihedral_angle_3_deg 15.968 r_dihedral_angle_1_deg 6.316 r_long_range_B_other 4.938 r_long_range_B_refined 4.937 r_scangle_other 3.356 r_mcangle_it 3.031 r_mcangle_other 3.031 r_scbond_it 2.083 r_scbond_other 2.083 r_mcbond_it 1.95 r_mcbond_other 1.949 r_angle_refined_deg 1.441 r_angle_other_deg 0.933 r_chiral_restr 0.079 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 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 7052 Nucleic Acid Atoms Solvent Atoms 267 Heterogen Atoms 104
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing