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Flavin-dependent tryptophan 6-halogenase Thal in complex with a D-Trp-Ser dipeptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6H43
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9 293 Reservoir solution: 100 mM Bicine pH 9.0, 1.6 M KH2PO4/K2HPO4; Protein concentration: 15 mg/ml; Protein buffer: 10 mM Tris pH 7.4, 50 mM NaCl, 1 mM DTT; Drop ratio: 1:1
Crystal Properties Matthews coefficient Solvent content 3.25 62.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 137.2 α = 90 b = 137.2 β = 90 c = 143.8 γ = 120
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 2M 2020-03-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.9184 BESSY 14.2
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 2.95 47.98 100 0.154 0.998 16.71 10.54 32396 69
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 2.95 3.03 100 1.54 0.676 1.99 11.03
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 FREE R-VALUE 6H43 2.95 47.98 30787 1577 99.92 0.19528 0.19244 0.1946 0.24988 0.2488 RANDOM 70.78
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] 1.23 0.62 1.23 -4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.401 r_dihedral_angle_4_deg 17.188 r_dihedral_angle_3_deg 16.326 r_long_range_B_refined 11.792 r_long_range_B_other 11.792 r_mcangle_it 9.106 r_mcangle_other 9.104 r_scangle_other 8.95 r_dihedral_angle_1_deg 7.5 r_mcbond_it 6.137
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.401 r_dihedral_angle_4_deg 17.188 r_dihedral_angle_3_deg 16.326 r_long_range_B_refined 11.792 r_long_range_B_other 11.792 r_mcangle_it 9.106 r_mcangle_other 9.104 r_scangle_other 8.95 r_dihedral_angle_1_deg 7.5 r_mcbond_it 6.137 r_mcbond_other 6.135 r_scbond_it 5.947 r_scbond_other 5.94 r_angle_refined_deg 1.465 r_angle_other_deg 1.217 r_chiral_restr 0.064 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 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 8297 Nucleic Acid Atoms Solvent Atoms 6 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing