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Crystal structure of Vibrio cholerae 5'-methylthioadenosine/S-adenosyl homocysteine nucleosidase (MTAN) complexed with methylthio-DADMe-Immucillin-A
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 295 Protein (10 mg/mL); Reservoir (0.1M di-ammonium hydrogen citrate and 15% PEG 3350); Cryoprotection (20% (v/v) glycerol)
Crystal Properties Matthews coefficient Solvent content 2.11 41.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.192 α = 90 b = 72.002 β = 110.32 c = 61.648 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 ADSC QUANTUM 315r 2014-08-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.075 NSLS X29A
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 1.37 50 93 0.048 16.2 3.9 85031 10.2
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 1.37 1.39 99.1 0.22 6.77 3.5 4510
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 3DP9 1.37 30 80872 4126 92.95 0.1654 0.1645 0.183 0.2093 RANDOM 13.758
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] 1.23 -0.69 -0.34 -0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.684 r_dihedral_angle_3_deg 10.675 r_dihedral_angle_4_deg 10.599 r_dihedral_angle_1_deg 5.959 r_angle_refined_deg 1.367 r_mcangle_it 1.199 r_angle_other_deg 0.755 r_mcbond_it 0.724 r_mcbond_other 0.724 r_chiral_restr 0.076
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.684 r_dihedral_angle_3_deg 10.675 r_dihedral_angle_4_deg 10.599 r_dihedral_angle_1_deg 5.959 r_angle_refined_deg 1.367 r_mcangle_it 1.199 r_angle_other_deg 0.755 r_mcbond_it 0.724 r_mcbond_other 0.724 r_chiral_restr 0.076 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3535 Nucleic Acid Atoms Solvent Atoms 431 Heterogen Atoms 40
Software Software Software Name Purpose DENZO data reduction REFMAC refinement PDB_EXTRACT data extraction SCALEPACK data scaling MOLREP phasing