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Crystal structure of Scabin, a mono-ADP-ribosyltransferase from Streptomyces scabies
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CB4 PDB entry 2CB4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 100 mM MES, pH 6.5, 15% PEG400
Crystal Properties Matthews coefficient Solvent content 2.29 46.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.787 α = 90 b = 61.075 β = 99.64 c = 37.812 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 CCD RAYONIX MX-300 2014-04-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.979 CLSI 08ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.45 43.273 94.4 0.042 0.048 18.81 33118 -3 26.76
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.45 1.54 81 0.764 0.876 2.15
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 PDB entry 2CB4 1.45 43.27 31437 1655 94.75 0.1668 0.1649 0.1645 0.2021 0.202 RANDOM 27.961
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] -0.18 0.5 0.04 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.384 r_dihedral_angle_4_deg 19.897 r_dihedral_angle_3_deg 13.359 r_dihedral_angle_1_deg 8.317 r_mcangle_it 3.538 r_angle_refined_deg 2.81 r_mcbond_it 2.346 r_mcbond_other 2.335 r_angle_other_deg 1.366 r_chiral_restr 0.166
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.384 r_dihedral_angle_4_deg 19.897 r_dihedral_angle_3_deg 13.359 r_dihedral_angle_1_deg 8.317 r_mcangle_it 3.538 r_angle_refined_deg 2.81 r_mcbond_it 2.346 r_mcbond_other 2.335 r_angle_other_deg 1.366 r_chiral_restr 0.166 r_bond_refined_d 0.033 r_gen_planes_refined 0.017 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1313 Nucleic Acid Atoms Solvent Atoms 177 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling PDB_EXTRACT data extraction MOLREP phasing