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The crystal structure of isothiocyanate hydrolase from Delia radicum gut bacteria
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3RPC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 286 0.2M calcium acetate,
0.1M HEPES:NaOH,
10% (w/v) PEG8000
Crystal Properties Matthews coefficient Solvent content 2.67 53.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 179.163 α = 90 b = 79.526 β = 89.98 c = 90.408 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 PIXEL DECTRIS PILATUS3 6M Mirror 2017-07-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97918 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.55 50 97.9 0.113 0.134 0.072 10.8 3.4 81359 -3 43.54
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.55 2.59 88.1 0.724 0.867 0.471 0.786 1.28 3.2
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 3RPC 2.55 49.84 77269 4076 97.58 0.20749 0.20558 0.221 0.24335 0.2621 RANDOM 57.479
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] -19.11 8.03 76.9 -57.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.081 r_dihedral_angle_3_deg 15.77 r_dihedral_angle_4_deg 14.879 r_dihedral_angle_1_deg 5.994 r_long_range_B_refined 3.627 r_long_range_B_other 3.627 r_mcangle_it 2.357 r_mcangle_other 2.356 r_scangle_other 1.914 r_angle_refined_deg 1.865
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.081 r_dihedral_angle_3_deg 15.77 r_dihedral_angle_4_deg 14.879 r_dihedral_angle_1_deg 5.994 r_long_range_B_refined 3.627 r_long_range_B_other 3.627 r_mcangle_it 2.357 r_mcangle_other 2.356 r_scangle_other 1.914 r_angle_refined_deg 1.865 r_mcbond_it 1.39 r_mcbond_other 1.39 r_scbond_it 1.085 r_scbond_other 1.084 r_angle_other_deg 0.875 r_chiral_restr 0.064 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16322 Nucleic Acid Atoms Solvent Atoms 42 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling HKL-3000 phasing