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Crystal structure of Helicobacter pylori 5'-methylthioadenosine/S-adenosyl homocysteine nucleosidase (MTAN) complexed with (((4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl)(hexyl)amino)methanol
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 malonate pH 7.0 and 20 % (w/v) PEG 3350); Cryoprotection (20% (v/v) glycerol)
Crystal Properties Matthews coefficient Solvent content 2.54 51.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.091 α = 90 b = 69.446 β = 113.08 c = 65.566 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 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 2.1 50 99.8 0.073 10.9 3.7 31369 36.7
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 2.1 2.14 99.3 0.588 2.32 3.3 1536
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 2.1 25 29762 1578 99.66 0.1891 0.1873 0.2004 0.2241 0.2352 RANDOM 37.684
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] -1.12 -3.27 4.75 -0.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.585 r_dihedral_angle_4_deg 19.369 r_dihedral_angle_3_deg 15.07 r_dihedral_angle_1_deg 6.004 r_mcangle_it 2.893 r_mcbond_other 1.959 r_mcbond_it 1.958 r_angle_refined_deg 1.413 r_angle_other_deg 0.768 r_chiral_restr 0.075
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.585 r_dihedral_angle_4_deg 19.369 r_dihedral_angle_3_deg 15.07 r_dihedral_angle_1_deg 6.004 r_mcangle_it 2.893 r_mcbond_other 1.959 r_mcbond_it 1.958 r_angle_refined_deg 1.413 r_angle_other_deg 0.768 r_chiral_restr 0.075 r_bond_refined_d 0.01 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 3636 Nucleic Acid Atoms Solvent Atoms 100 Heterogen Atoms 41
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-3000 phasing