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Crystal structure of 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase from Salmonella enterica with butyl-thio-DADMe-Immucillin-A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 20% PEG 3350, 0.2M lithium acetate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.94 36.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.05 α = 90 b = 46.61 β = 114.78 c = 70.94 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 Rosenbaum-Rock double crystal sagittal focusing monochrometer and vertical focusing mirror 2012-02-09 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 1.93 64.41 99.7 0.069 0.069 11.7 4 30569 30569 19.7
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 1.93 2.03 99.4 0.253 0.253 4.2 3.9 4402
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 (All) 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 1.93 37.46 30557 29019 1538 99.61 0.18782 0.18782 0.18549 0.1944 0.2327 0.2361 RANDOM 27.045
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] -2.72 -1.02 2.13 -0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.374 r_dihedral_angle_4_deg 25.658 r_dihedral_angle_3_deg 13.041 r_dihedral_angle_1_deg 5.977 r_angle_refined_deg 1.385 r_angle_other_deg 0.764 r_chiral_restr 0.078 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.374 r_dihedral_angle_4_deg 25.658 r_dihedral_angle_3_deg 13.041 r_dihedral_angle_1_deg 5.977 r_angle_refined_deg 1.385 r_angle_other_deg 0.764 r_chiral_restr 0.078 r_bond_refined_d 0.009 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 3404 Nucleic Acid Atoms Solvent Atoms 161 Heterogen Atoms 58
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling