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Crystal structure of MibH, a lathipeptide tryptophan 5-halogenase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WET
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 289 12.5% MPD, 12.5% PEG 3.35K, 0.1 M MES/imidazole pH 6.5, and 0.09 M NPS (1:1:1 NaNO3, Na2HPO4, (NH4)2SO4)
Crystal Properties Matthews coefficient Solvent content 2.25 45.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.436 α = 64.58 b = 87.887 β = 69.9 c = 100.632 γ = 76.26
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 2016-02-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97857 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.88 87.38 97.8 16.8 7.9 170761
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 2WET 1.88 87.38 155653 8242 97.77 0.15855 0.15618 0.1615 0.20362 0.207 RANDOM 36.207
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] 1.18 1.63 -1.95 -2.4 -0.4 0.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.054 r_dihedral_angle_4_deg 20.071 r_dihedral_angle_3_deg 15.442 r_long_range_B_refined 9.389 r_long_range_B_other 9.266 r_dihedral_angle_1_deg 6.925 r_scangle_other 6.463 r_scbond_it 4.336 r_scbond_other 4.335 r_mcangle_other 4.322
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.054 r_dihedral_angle_4_deg 20.071 r_dihedral_angle_3_deg 15.442 r_long_range_B_refined 9.389 r_long_range_B_other 9.266 r_dihedral_angle_1_deg 6.925 r_scangle_other 6.463 r_scbond_it 4.336 r_scbond_other 4.335 r_mcangle_other 4.322 r_mcangle_it 4.321 r_mcbond_other 3.177 r_mcbond_it 3.176 r_angle_refined_deg 1.942 r_angle_other_deg 0.947 r_chiral_restr 0.122 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 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 15908 Nucleic Acid Atoms Solvent Atoms 1347 Heterogen Atoms 108
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing