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Crystal structure of 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase from Salmonella enterica with methyl-thio-DADMe-Immucillin-A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 35% 2-methyl-2,4-pentanediol, 0.2M sodium chloride, 0.1M Tris, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.53 51.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.41 α = 90 b = 82.54 β = 90 c = 93.11 γ = 90
Symmetry Space Group P 21 21 21
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 Rosenbaum-Rock double crystal sagittal focusing monochrometer and vertical focusing mirror 2011-02-09 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) R Sym 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 61.77 99 0.196 0.196 6.7 6.7 36435 36435
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.11 96.8 0.347 0.347 4.1 6.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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 2 46.18 36380 34563 1817 98.77 0.17911 0.17717 0.1847 0.21597 0.2229 RANDOM 16.933
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] -0.41 -0.48 0.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.143 r_dihedral_angle_4_deg 17.634 r_dihedral_angle_3_deg 12.91 r_dihedral_angle_1_deg 6.111 r_angle_refined_deg 1.452 r_angle_other_deg 1.034 r_chiral_restr 0.082 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.143 r_dihedral_angle_4_deg 17.634 r_dihedral_angle_3_deg 12.91 r_dihedral_angle_1_deg 6.111 r_angle_refined_deg 1.452 r_angle_other_deg 1.034 r_chiral_restr 0.082 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.004 r_gen_planes_other 0.001 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_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it 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 3467 Nucleic Acid Atoms Solvent Atoms 271 Heterogen Atoms 66
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling