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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 6.3 295 Protein (10 mg/mL); Reservoir (0.2M ammonium chloride pH 6.3 and 20% PEG 3350); Cryoprotection (20% (v/v) glycerol)
Crystal Properties Matthews coefficient Solvent content 2.2 44.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.898 α = 90 b = 72.708 β = 110 c = 61.621 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 RAYONIX MX225HE 2014-11-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.9793 APS 31-ID
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 1.5 50 99.1 0.082 8.9 3.6 69602 13.2
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 1.5 1.53 96.8 0.685 1.78 3.5 3351
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 1.5 30 66097 3448 99.09 0.1696 0.1687 0.1698 0.1866 0.1878 RANDOM 17.318
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 -0.24 -0.12 -0.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.259 r_dihedral_angle_4_deg 13.133 r_dihedral_angle_3_deg 11.333 r_dihedral_angle_1_deg 5.866 r_angle_refined_deg 1.455 r_mcangle_it 1.403 r_angle_other_deg 0.972 r_mcbond_it 0.874 r_mcbond_other 0.874 r_chiral_restr 0.154
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.259 r_dihedral_angle_4_deg 13.133 r_dihedral_angle_3_deg 11.333 r_dihedral_angle_1_deg 5.866 r_angle_refined_deg 1.455 r_mcangle_it 1.403 r_angle_other_deg 0.972 r_mcbond_it 0.874 r_mcbond_other 0.874 r_chiral_restr 0.154 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3509 Nucleic Acid Atoms Solvent Atoms 360 Heterogen Atoms 50
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction