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Flavin-dependent tryptophan halogenase Thal: N-terminally His-tagged form of quintuple mutant (NHis-Thal-RebH5)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6H43 6H43 chain A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9 293.5 reservoir solution: 0.1 M bicine pH 9.0, 20 % (w/v) PEG 4000, 10 % (v/v) glycerol, 0.02 M amino acid mix consisting of L-Glu, L-Ala, D-Ala, Gly, L-Lys, D-Lysis, L-Ser and D-Ser;
protein buffer solution: 10 mM TRIS, 50 mM NaCl, 1 mM TCEP;
protein concentration: ~15 mg/mL;
drop ratio: 100 nL+100 nL (protein + reservoir)
Crystal Properties Matthews coefficient Solvent content 2.3 46.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.58 α = 90 b = 118.57 β = 104.038 c = 87.1 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 PILATUS 6M 2018-06-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.9763 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) CC (Half) 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 1.63 50 96.6 0.079 0.999 15.33 7.03 129082 31.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.63 1.67 85.3 1.146 0.748 1.97 6.73
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6H43 chain A 1.63 48.579 129047 6474 96.564 0.168 0.1667 0.2023 0.2137 27.22
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] 1.086 -0.784 -0.923 0.203
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.203 r_dihedral_angle_4_deg 16.405 r_dihedral_angle_3_deg 11.837 r_dihedral_angle_1_deg 6.768 r_lrange_other 6.339 r_lrange_it 6.338 r_scangle_it 4.581 r_scangle_other 4.579 r_mcangle_other 3.198 r_mcangle_it 3.197
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.203 r_dihedral_angle_4_deg 16.405 r_dihedral_angle_3_deg 11.837 r_dihedral_angle_1_deg 6.768 r_lrange_other 6.339 r_lrange_it 6.338 r_scangle_it 4.581 r_scangle_other 4.579 r_mcangle_other 3.198 r_mcangle_it 3.197 r_scbond_it 3.056 r_scbond_other 3.054 r_mcbond_it 2.356 r_mcbond_other 2.343 r_angle_refined_deg 1.595 r_angle_other_deg 1.457 r_symmetry_nbd_refined 0.299 r_nbd_refined 0.22 r_nbd_other 0.196 r_symmetry_nbd_other 0.179 r_nbtor_refined 0.172 r_xyhbond_nbd_refined 0.159 r_symmetry_xyhbond_nbd_refined 0.134 r_chiral_restr 0.084 r_ncsr_local_group_1 0.081 r_symmetry_nbtor_other 0.079 r_symmetry_xyhbond_nbd_other 0.055 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8383 Nucleic Acid Atoms Solvent Atoms 975 Heterogen Atoms 88
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing