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Crystal structure of Helicobacter pylori 5'-methylthioadenosine/S-adenosyl homocysteine nucleosidase (MTAN) complexed with pyrazinylthio-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 3.03 59.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 157.512 α = 90 b = 157.512 β = 90 c = 157.512 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 2014-08-28 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 1.9 50 100 0.146 6.6 31.7 26571 18.8
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 1.9 1.93 100 0.719 23.1 1281
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 2 25 21421 1076 98.59 0.1763 0.1753 0.1867 0.1952 0.2046 RANDOM 24.827
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 36.737 r_dihedral_angle_4_deg 15.851 r_dihedral_angle_3_deg 13.783 r_dihedral_angle_1_deg 5.901 r_mcangle_it 1.948 r_angle_refined_deg 1.452 r_mcbond_it 1.312 r_mcbond_other 1.285 r_angle_other_deg 0.78 r_chiral_restr 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.737 r_dihedral_angle_4_deg 15.851 r_dihedral_angle_3_deg 13.783 r_dihedral_angle_1_deg 5.901 r_mcangle_it 1.948 r_angle_refined_deg 1.452 r_mcbond_it 1.312 r_mcbond_other 1.285 r_angle_other_deg 0.78 r_chiral_restr 0.08 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1753 Nucleic Acid Atoms Solvent Atoms 194 Heterogen Atoms 44
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction