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Crystal structure of MTA/AdoHcy nucleosidase with a ligand-free purine binding site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JYS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 ammonium sulfate, PEG 2000 MME, sodium HEPES, isopropanol, QX-10000024, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.9 57.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.01 α = 90 b = 127.52 β = 90 c = 69.59 γ = 90
Symmetry Space Group C 2 2 2
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 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 31.27 0.056 9.8 21178 21178 31.8
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 2 2.07 97.4 0.346 9.6
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 (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 1JYS 2 31.27 21178 21178 2089 98.5 0.206 0.206 0.2109 0.234 0.2409 RANDOM 33.1
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] -5.12 6.11 -1
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.1 c_scangle_it 4.34 c_scbond_it 3.19 c_mcangle_it 2.47 c_mcbond_it 1.87 c_angle_deg 1.7 c_improper_angle_d 0.97 c_bond_d 0.011 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.1 c_scangle_it 4.34 c_scbond_it 3.19 c_mcangle_it 2.47 c_mcbond_it 1.87 c_angle_deg 1.7 c_improper_angle_d 0.97 c_bond_d 0.011 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1696 Nucleic Acid Atoms Solvent Atoms 146 Heterogen Atoms 36
Software Software Software Name Purpose CrystalClear data collection d*TREK data reduction CNS refinement CrystalClear data reduction d*TREK data scaling CNS phasing