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Crystal structure of Helicobacter pylori 5'-methylthioadenosine/S-adenosyl homocysteine nucleosidase (MTAN) complexed with 2-(2-hydroxyethoxy)ethylthiomethyl-DADMe-Immucillin-A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4FFS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 Protein (10 mg/mL); Reservoir (0.2 M sodium fluoride and 2.2 M ammonium sulfate); Cryoprotection (20% (v/v) glycerol)
Crystal Properties Matthews coefficient Solvent content 2.21 44.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.706 α = 90 b = 74.078 β = 90 c = 176.328 γ = 90
Symmetry Space Group P 21 21 21
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 2014-06-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.075 NSLS X29A
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 1.58 50 98.4 0.107 7.8 7.8 128267 12.8
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 1.58 1.61 94.3 0.874 2.27 7.3 6101
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 4FFS 1.58 25 121480 6438 98.37 0.1859 0.1845 0.2131 0.2098 RANDOM 15.966
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] 0.21 0.47 -0.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.838 r_dihedral_angle_4_deg 13.259 r_dihedral_angle_3_deg 12.842 r_dihedral_angle_1_deg 5.607 r_angle_refined_deg 1.33 r_mcangle_it 1.286 r_mcbond_it 0.791 r_mcbond_other 0.789 r_angle_other_deg 0.753 r_chiral_restr 0.072
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.838 r_dihedral_angle_4_deg 13.259 r_dihedral_angle_3_deg 12.842 r_dihedral_angle_1_deg 5.607 r_angle_refined_deg 1.33 r_mcangle_it 1.286 r_mcbond_it 0.791 r_mcbond_other 0.789 r_angle_other_deg 0.753 r_chiral_restr 0.072 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7017 Nucleic Acid Atoms Solvent Atoms 661 Heterogen Atoms 118
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction