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Crystal structure of 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase from Salmonella enterica with homocysteine-DADMe-Immucillin-A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 12% PEG 20000, 0.1M MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.16 43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.49 α = 90 b = 70.49 β = 90 c = 122.83 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 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 1.85 61.41 99.8 0.153 0.153 5.3 39679 39679 9.5
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 1.85 1.95 99.6 0.865 0.865 3.2 5.1 5700
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 1.85 39.93 39608 37617 1991 99.72 0.1795 0.1795 0.17755 0.1851 0.21477 0.2218 RANDOM 22.307
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] -0.17 2.42 -2.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.355 r_dihedral_angle_4_deg 21.375 r_dihedral_angle_3_deg 12.665 r_dihedral_angle_1_deg 6.009 r_angle_refined_deg 1.38 r_angle_other_deg 1.112 r_chiral_restr 0.079 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 37.355 r_dihedral_angle_4_deg 21.375 r_dihedral_angle_3_deg 12.665 r_dihedral_angle_1_deg 6.009 r_angle_refined_deg 1.38 r_angle_other_deg 1.112 r_chiral_restr 0.079 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.004 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3404 Nucleic Acid Atoms Solvent Atoms 247 Heterogen Atoms 60
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling