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Crystal Structure of Arabidopsis thaliana 5'-Methylthioadenosine nucleosidase in complex with Formycin A
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 1.97 37.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.3 α = 90 b = 127.05 β = 109.63 c = 45.45 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 MIRRORS 2005-06-30 M SINGLE WAVELENGTH 2 1 x-ray M
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300
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 1,2 1.93 23.61 94.8 0.06 12.6 3.17 31340
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) 1,2 1.93 2 90.5 0.155 5.2 2.48
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 MAD THROUGHOUT 1.93 23.61 28208 3131 94.7 0.17771 0.17158 0.1723 0.23275 0.2336 RANDOM 19.226
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] 2.58 0.51 -1.2 -1.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.712 r_dihedral_angle_3_deg 13.697 r_dihedral_angle_4_deg 7.623 r_dihedral_angle_1_deg 5.818 r_scangle_it 2.868 r_scbond_it 1.903 r_angle_refined_deg 1.509 r_mcangle_it 1.116 r_mcbond_it 0.636 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.712 r_dihedral_angle_3_deg 13.697 r_dihedral_angle_4_deg 7.623 r_dihedral_angle_1_deg 5.818 r_scangle_it 2.868 r_scbond_it 1.903 r_angle_refined_deg 1.509 r_mcangle_it 1.116 r_mcbond_it 0.636 r_nbtor_refined 0.302 r_nbd_refined 0.228 r_symmetry_vdw_refined 0.183 r_xyhbond_nbd_refined 0.14 r_symmetry_hbond_refined 0.111 r_chiral_restr 0.101 r_bond_refined_d 0.014 r_gen_planes_refined 0.004 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 3687 Nucleic Acid Atoms Solvent Atoms 440 Heterogen Atoms 33
Software Software Software Name Purpose d*TREK data scaling REFMAC refinement PDB_EXTRACT data extraction d*TREK data reduction SOLVE phasing