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Crystal structure of 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase from Salmonella enterica with Adenine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3O4V pdb entry 3O4V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 1.0M (NH4)2HPO4, 0.1M Imidazole, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.92 35.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.05 α = 90 b = 68.12 β = 90 c = 89.66 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 2011-08-25 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 1.36 54.24 100 0.112 0.112 12.9 11.5 87459 87459 12.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.36 1.43 99.9 2.6 11.2 12605
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 pdb entry 3O4V 1.36 41.95 87381 83002 4379 99.94 0.11455 0.11455 0.11286 0.1118 0.14597 0.1458 RANDOM 15.932
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] -0.63 -0.04 0.68
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 38.373 r_dihedral_angle_2_deg 36.4 r_dihedral_angle_4_deg 19.272 r_dihedral_angle_3_deg 11.74 r_sphericity_bonded 10.401 r_dihedral_angle_1_deg 5.584 r_rigid_bond_restr 2.186 r_angle_refined_deg 1.435 r_angle_other_deg 0.812 r_chiral_restr 0.092
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 38.373 r_dihedral_angle_2_deg 36.4 r_dihedral_angle_4_deg 19.272 r_dihedral_angle_3_deg 11.74 r_sphericity_bonded 10.401 r_dihedral_angle_1_deg 5.584 r_rigid_bond_restr 2.186 r_angle_refined_deg 1.435 r_angle_other_deg 0.812 r_chiral_restr 0.092 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3445 Nucleic Acid Atoms Solvent Atoms 386 Heterogen Atoms 114
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling