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Crystal structure of 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase in complex with adenine from Vibrio fischeri ES114
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, SITTING DROP 7 290 0.2 M CaCl2, 0.1 M HEPES, 20% PEG6000
Crystal Properties Matthews coefficient Solvent content 2.19 43.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.642 α = 90 b = 72.915 β = 109.6 c = 57.563 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 CCD MARMOSAIC 225 mm CCD beryllium lenses 2016-11-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 1.14 30 92.2 0.06 0.79 33.2 4.4 144464
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 1.14 1.16 90.6 0.57 2.1 4
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 3DP9 1.14 30 137008 7428 92.09 0.13059 0.12911 0.1369 0.15785 0.1644 RANDOM 16.867
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] -0.59 -0.16 -0.37 0.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.651 r_sphericity_free 20.89 r_dihedral_angle_4_deg 17.648 r_dihedral_angle_3_deg 11.997 r_sphericity_bonded 10.485 r_dihedral_angle_1_deg 6.442 r_rigid_bond_restr 4.966 r_long_range_B_refined 4.021 r_long_range_B_other 3.932 r_scangle_other 2.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.651 r_sphericity_free 20.89 r_dihedral_angle_4_deg 17.648 r_dihedral_angle_3_deg 11.997 r_sphericity_bonded 10.485 r_dihedral_angle_1_deg 6.442 r_rigid_bond_restr 4.966 r_long_range_B_refined 4.021 r_long_range_B_other 3.932 r_scangle_other 2.86 r_scbond_it 2.573 r_scbond_other 2.569 r_angle_refined_deg 2.002 r_mcangle_it 1.607 r_mcangle_other 1.607 r_mcbond_it 1.299 r_mcbond_other 1.296 r_angle_other_deg 1.116 r_chiral_restr 0.289 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 r_bond_other_d 0.002 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3463 Nucleic Acid Atoms Solvent Atoms 682 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing