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2.1 Angstrom Resolution Crystal Structure of 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase (mtnN) from Haemophilus influenzae PittII.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3O4V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.3 295 Protein: 14.5 mg/ml, 0.01M Tris pH 8.3;
Screen: Classics II (B5), 1.26M Sodium phosphate, 0.14M Potassium phosphate;
Cryo: 1:1, reservoir : 50% Sucrose.
Crystal Properties Matthews coefficient Solvent content 3.35 63.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 124.536 α = 90 b = 214.743 β = 90 c = 146.904 γ = 90
Symmetry Space Group C 2 2 21
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 300 mm CCD C(111) 2017-07-12 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) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 2.1 30 100 0.081 0.081 0.089 0.035 19.8 6.2 115902 -3 38.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.14 100 0.74 0.74 0.806 0.318 0.807 2.7 6.3
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3o4v 2.1 29.87 108746 5621 99.92 0.1618 0.1603 0.1907 0.2201 RANDOM 44.826
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] -0.8 -2.38 3.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.623 r_dihedral_angle_4_deg 14.198 r_dihedral_angle_3_deg 10.014 r_dihedral_angle_1_deg 4.116 r_angle_refined_deg 1.363 r_angle_other_deg 0.325 r_gen_planes_refined 0.057 r_gen_planes_other 0.056 r_chiral_restr 0.055 r_bond_refined_d 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.623 r_dihedral_angle_4_deg 14.198 r_dihedral_angle_3_deg 10.014 r_dihedral_angle_1_deg 4.116 r_angle_refined_deg 1.363 r_angle_other_deg 0.325 r_gen_planes_refined 0.057 r_gen_planes_other 0.056 r_chiral_restr 0.055 r_bond_refined_d 0.006 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10256 Nucleic Acid Atoms Solvent Atoms 784 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction HKL-3000 data scaling MoRDa phasing