☰ Navigation Tabs
Structure of Arabidopsis thaliana 5'-Methylthioadenosine nucleosidase in apo form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Formycin-A complexed structure of A. thaliana MTAN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 295 NH4Cl, PEG3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 1.95 36.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.25 α = 90 b = 126.91 β = 106.75 c = 45.34 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 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 2 63.5 94.6 0.081 8.9 3.2 28189 31.5
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) 2 2.06 90.7 0.262 4 3.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 Formycin-A complexed structure of A. thaliana MTAN 2 63.5 25315 2851 94.46 0.20341 0.19759 0.1984 0.25377 0.255 RANDOM 27.2
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] 2.22 2.12 -2.33 1.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.776 r_dihedral_angle_3_deg 15.914 r_dihedral_angle_4_deg 13.64 r_dihedral_angle_1_deg 10.017 r_scangle_it 3.27 r_scbond_it 2.238 r_mcangle_it 1.654 r_angle_refined_deg 1.498 r_mcbond_it 1.121 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.776 r_dihedral_angle_3_deg 15.914 r_dihedral_angle_4_deg 13.64 r_dihedral_angle_1_deg 10.017 r_scangle_it 3.27 r_scbond_it 2.238 r_mcangle_it 1.654 r_angle_refined_deg 1.498 r_mcbond_it 1.121 r_nbtor_refined 0.31 r_nbd_refined 0.228 r_symmetry_vdw_refined 0.213 r_xyhbond_nbd_refined 0.178 r_symmetry_hbond_refined 0.142 r_chiral_restr 0.106 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 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 3715 Nucleic Acid Atoms Solvent Atoms 260 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection d*TREK data reduction d*TREK data scaling PHASER phasing