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Crystal Structure of Arabidopsis thaliana 5'-Methylthioadenosine nucleosidase in complex with 5'-methylthiotubercidin
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 295 NH4I, PEG3350, ethylene glycol, pH 7.5, vapor diffusion, hanging drop, temperature 295K, pH 7.50
Crystal Properties Matthews coefficient Solvent content 1.93 36.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.58 α = 90 b = 126.05 β = 109.02 c = 45.54 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 IMAGE PLATE RIGAKU RAXIS IV MIRRORS 2004-11-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.84 32.77 95.5 0.06 16.2 6.36 35711 22.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.84 1.91 97.3 0.299 5.7 6.81
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.84 32.77 35709 1790 95.5 0.185 0.185 0.1834 0.19 0.1899 RANDOM 22.83
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] 1.76 1.62 -1.07 0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.781 r_dihedral_angle_3_deg 13.569 r_dihedral_angle_4_deg 10.56 r_dihedral_angle_1_deg 10.168 r_scangle_it 3.376 r_angle_refined_deg 2.714 r_scbond_it 2.311 r_mcangle_it 1.415 r_mcbond_it 0.872 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.781 r_dihedral_angle_3_deg 13.569 r_dihedral_angle_4_deg 10.56 r_dihedral_angle_1_deg 10.168 r_scangle_it 3.376 r_angle_refined_deg 2.714 r_scbond_it 2.311 r_mcangle_it 1.415 r_mcbond_it 0.872 r_nbtor_refined 0.302 r_symmetry_vdw_refined 0.261 r_nbd_refined 0.237 r_xyhbond_nbd_refined 0.235 r_symmetry_hbond_refined 0.142 r_chiral_restr 0.115 r_bond_refined_d 0.018 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3672 Nucleic Acid Atoms Solvent Atoms 351 Heterogen Atoms 48
Software Software Software Name Purpose d*TREK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction d*TREK data reduction