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Flavin-dependent tryptophan 6-halogenase Thal in complex with tryptophan and FAD
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 8.4 293.5 reservoir: 0.1M bicine pH 8.4, 1.6M K2HPO4/KH2PO4
protein concentration: ~15mg/mL
drop ratio: 2:1 (P:R)
protein buffer: 10 mM Tris pH 8.4, 50 mM NaCl and 1 mM TCEP
Crystal Properties Matthews coefficient Solvent content 3.29 62.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 138.25 α = 90 b = 138.25 β = 90 c = 142.01 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 6M-F 2017-11-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 1.0 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 2.7 50 100 0.172 0.181 0.056 0.998 14.6 20.7 42328 63.553
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 2.7 2.8 100 1.696 1.785 0.556 0.775 2.1 20.4
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 6H43 2.7 49.58 40099 2195 99.98 0.1886 0.1857 0.1883 0.2442 0.243 RANDOM 69.882
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] 0.72 0.36 0.72 -2.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.744 r_dihedral_angle_4_deg 18.222 r_dihedral_angle_3_deg 17.651 r_dihedral_angle_1_deg 7.474 r_angle_refined_deg 1.588 r_angle_other_deg 1.245 r_chiral_restr 0.067 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.744 r_dihedral_angle_4_deg 18.222 r_dihedral_angle_3_deg 17.651 r_dihedral_angle_1_deg 7.474 r_angle_refined_deg 1.588 r_angle_other_deg 1.245 r_chiral_restr 0.067 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8404 Nucleic Acid Atoms Solvent Atoms 75 Heterogen Atoms 142
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling PHASER phasing