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Crystal structure of Helicobacter pylori 5'-methylthioadenosine/S-adenosyl homocysteine nucleosidase (MTAN) complexed with methylthio-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 9 295 Protein (10 mg/mL); Reservoir (0.1 M Bicine pH 9.0 and 2.4 M ammonium sulfate); Cryoprotection (20% (v/v) glycerol)
Crystal Properties Matthews coefficient Solvent content 3 58.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 156.958 α = 90 b = 156.958 β = 90 c = 156.958 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 2 50 100 0.116 0.117 0.018 7.2 39.8 22676 20.9
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 2 2.03 100 0.811 0.822 0.133 0.966 5.79 38 1117
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 21409 1159 99.89 0.1625 0.1616 0.1725 0.1786 0.1856 RANDOM 25.386
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 32.521 r_dihedral_angle_4_deg 15.097 r_dihedral_angle_3_deg 13.335 r_dihedral_angle_1_deg 5.687 r_angle_refined_deg 1.256 r_mcangle_it 1.112 r_angle_other_deg 0.747 r_mcbond_it 0.709 r_mcbond_other 0.699 r_chiral_restr 0.069
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.521 r_dihedral_angle_4_deg 15.097 r_dihedral_angle_3_deg 13.335 r_dihedral_angle_1_deg 5.687 r_angle_refined_deg 1.256 r_mcangle_it 1.112 r_angle_other_deg 0.747 r_mcbond_it 0.709 r_mcbond_other 0.699 r_chiral_restr 0.069 r_bond_refined_d 0.008 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 1753 Nucleic Acid Atoms Solvent Atoms 149 Heterogen Atoms 20
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction