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Flavin-dependent Tryptophan 6-halogenase Thal
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OAM 2OAM, 2AQJ, 2WEU, 5HY5 experimental model PDB 2AQJ 2OAM, 2AQJ, 2WEU, 5HY5 experimental model PDB 2WEU 2OAM, 2AQJ, 2WEU, 5HY5 experimental model PDB 5HY5 2OAM, 2AQJ, 2WEU, 5HY5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 reservoir: 0.1 M Tris pH 8.5, 1.5 M K2HPO4/KH2PO4
protein concentration: ~ 15mg/mL
drop ratio: 2:1 (P:R)
protein buffer: 10 mM Tris pH 7.4, 50 mM NaCl and 1 mM TCEP
Crystal Properties Matthews coefficient Solvent content 3.25 62.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 139.47 α = 90 b = 139.47 β = 90 c = 142.51 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 2017-04-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.9 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 2.2 49.89 100 0.14 0.998 11.5 8.5 79654 52.9
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 2.2 2.26 100 1.841 0.634 2 8.4
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 2OAM, 2AQJ, 2WEU, 5HY5 2.2 49.89 75624 3990 99.97 0.17168 0.16966 0.1758 0.2111 0.2152 RANDOM 48.75
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] 0.53 0.26 0.53 -1.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.179 r_dihedral_angle_4_deg 19.72 r_dihedral_angle_3_deg 15.117 r_long_range_B_other 9.124 r_long_range_B_refined 9.121 r_scangle_other 7.403 r_dihedral_angle_1_deg 6.706 r_mcangle_it 5.714 r_mcangle_other 5.714 r_scbond_it 5.184
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.179 r_dihedral_angle_4_deg 19.72 r_dihedral_angle_3_deg 15.117 r_long_range_B_other 9.124 r_long_range_B_refined 9.121 r_scangle_other 7.403 r_dihedral_angle_1_deg 6.706 r_mcangle_it 5.714 r_mcangle_other 5.714 r_scbond_it 5.184 r_scbond_other 5.182 r_mcbond_other 4.118 r_mcbond_it 4.117 r_angle_refined_deg 1.457 r_angle_other_deg 0.931 r_chiral_restr 0.075 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 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 8376 Nucleic Acid Atoms Solvent Atoms 319 Heterogen Atoms 109
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing