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Crystal structure of 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase from Bacillus anthracis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DP9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 2M Ammonium sulfate, 0.2M MgCl2, Tris pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.99 38.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 181.269 α = 90 b = 74.635 β = 95.26 c = 46.688 γ = 90
Symmetry Space Group C 1 2 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 MAR scanner 345 mm plate 2013-10-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.7 50 95.4 0.08 21.64 4.2 16291 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.8 75 0.34 2.549 2.4
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 3DP9 2.7 34.49 23990 15438 819 94.89 0.24258 0.24104 0.2432 0.27145 0.2731 RANDOM 60.04
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] 1.01 -0.6 -1.95 1.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.796 r_dihedral_angle_4_deg 20.202 r_dihedral_angle_3_deg 16.528 r_dihedral_angle_1_deg 6.147 r_long_range_B_refined 2.634 r_long_range_B_other 2.634 r_mcangle_it 1.613 r_mcangle_other 1.613 r_angle_refined_deg 1.176 r_scangle_other 1.093
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.796 r_dihedral_angle_4_deg 20.202 r_dihedral_angle_3_deg 16.528 r_dihedral_angle_1_deg 6.147 r_long_range_B_refined 2.634 r_long_range_B_other 2.634 r_mcangle_it 1.613 r_mcangle_other 1.613 r_angle_refined_deg 1.176 r_scangle_other 1.093 r_angle_other_deg 1.048 r_mcbond_it 0.893 r_mcbond_other 0.893 r_scbond_it 0.562 r_scbond_other 0.562 r_chiral_restr 0.073 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d 0.003 r_gen_planes_other 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5265 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 54
Software Software Software Name Purpose MAR345dtb data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling