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Crystal structure of Helicobacter pylori 5'-methylthioadenosine/S-adenosyl homocysteine nucleosidase (MTAN) complexed with hydroxybutylthio-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 di-sodium phosphate and 2.2 M ammonium sulfate); Cryoprotection (20% (v/v) glycerol)
Crystal Properties Matthews coefficient Solvent content 3.01 59.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 157.256 α = 90 b = 157.256 β = 90 c = 157.256 γ = 90
Symmetry Space Group I 4 3 2
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 2014-06-05 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) Rrim I (All) Rpim I (All) 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 50 100 0.113 0.114 0.017 7.3 43.9 26379 16.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.93 100 0.876 0.886 0.136 0.966 5.86 41.9 1286
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 4FFS 1.9 25 25024 1338 99.91 0.1598 0.1583 0.17 0.1905 0.2047 RANDOM 19.999
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.626 r_dihedral_angle_4_deg 13.846 r_dihedral_angle_3_deg 13.083 r_dihedral_angle_1_deg 5.481 r_mcangle_it 1.484 r_angle_refined_deg 1.256 r_mcbond_it 0.921 r_mcbond_other 0.911 r_angle_other_deg 0.737 r_chiral_restr 0.069
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.626 r_dihedral_angle_4_deg 13.846 r_dihedral_angle_3_deg 13.083 r_dihedral_angle_1_deg 5.481 r_mcangle_it 1.484 r_angle_refined_deg 1.256 r_mcbond_it 0.921 r_mcbond_other 0.911 r_angle_other_deg 0.737 r_chiral_restr 0.069 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1756 Nucleic Acid Atoms Solvent Atoms 222 Heterogen Atoms 24
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction