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Crystal structure of staphylococcus aureus 5'-methylthioadenosine/s-adenosylhomocysteine nucleosidase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BL6 S AUREUS MTAN 3BL6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 4.2M FORMATE, 0.1M TRIS HCL, CRYOPROTECTANT 20% GLYCEROL, pH 8.50, VAPOR DIFFUSION, HANGING DROP, temperature 110K
Crystal Properties Matthews coefficient Solvent content 2.63 53.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.423 α = 90 b = 55.852 β = 90 c = 97.022 γ = 90
Symmetry Space Group P 2 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 110 CCD ADSC QUANTUM 210r 2007-07-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 Australian Synchrotron MX1
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 1.75 27.93 100 0.15 3.49 6.91 18068
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 2.11 100 0.66 1.23 6.87
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 S AUREUS MTAN 3BL6 2 26.72 17111 17111 919 99.92 0.18591 0.18343 0.1833 0.23305 0.233 RANDOM 25.331
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] 0.04 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.468 r_dihedral_angle_4_deg 17.48 r_dihedral_angle_3_deg 16.172 r_dihedral_angle_1_deg 6.987 r_angle_refined_deg 2.117 r_chiral_restr 0.165 r_bond_refined_d 0.032 r_gen_planes_refined 0.009 r_gen_planes_other 0.001 r_bond_other_d
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.468 r_dihedral_angle_4_deg 17.48 r_dihedral_angle_3_deg 16.172 r_dihedral_angle_1_deg 6.987 r_angle_refined_deg 2.117 r_chiral_restr 0.165 r_bond_refined_d 0.032 r_gen_planes_refined 0.009 r_gen_planes_other 0.001 r_bond_other_d r_angle_other_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1727 Nucleic Acid Atoms Solvent Atoms 138 Heterogen Atoms 12
Software Software Software Name Purpose MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling