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Crystal structure of Helicobacter pylori 5'-methylthioadenosine/S-adenosyl homocysteine nucleosidase (MTAN) complexed with (3R,4S)-1-((4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl)-4-((prop-2-yn-1-ylthio)methyl)pyrrolidin-3-ol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4WKP PDB entry 4WKP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 200 mM sodium nitrate, 20% w/v PEG3350
Crystal Properties Matthews coefficient Solvent content 2.2 44.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.255 α = 90 b = 73.255 β = 90 c = 176.142 γ = 90
Symmetry Space Group P 41 21 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 RAYONIX MX225HE KB mirrors 2017-11-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.97931 APS 31-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 1.6 67.64 100 0.999 13 14.4 64250
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.63 0.698
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 PDB entry 4WKP 1.6 67.64 60883 3258 99.99 0.16579 0.16433 0.1749 0.19342 0.2025 RANDOM 18.463
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] 0.03 0.03 -0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.604 r_dihedral_angle_4_deg 15.12 r_dihedral_angle_3_deg 12.813 r_dihedral_angle_1_deg 5.733 r_long_range_B_refined 4.9 r_long_range_B_other 4.9 r_scangle_other 2.712 r_scbond_it 1.706 r_scbond_other 1.705 r_mcangle_it 1.628
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.604 r_dihedral_angle_4_deg 15.12 r_dihedral_angle_3_deg 12.813 r_dihedral_angle_1_deg 5.733 r_long_range_B_refined 4.9 r_long_range_B_other 4.9 r_scangle_other 2.712 r_scbond_it 1.706 r_scbond_other 1.705 r_mcangle_it 1.628 r_mcangle_other 1.628 r_angle_refined_deg 1.473 r_mcbond_it 1.018 r_mcbond_other 1.016 r_angle_other_deg 0.926 r_chiral_restr 0.084 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3524 Nucleic Acid Atoms Solvent Atoms 530 Heterogen Atoms 82
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling PHASER phasing