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Flavin-dependent tryptophan 6-halogenase Thal in complex with D-Trp
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6H43 6H43 CHAINA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.2 293 RESERVOIR: 0.1 M BICINE PH 8.2, 1.6 M
K2HPO4/KH2PO4; PROTEIN CONCENTRATION: ~ 15 MG/ML; PROTEIN BUFFER: 10 MM TRIS PH 7.4, 50 MM NACL, 1 MM TCEP; PROTEIN AND SUBSTRATE D-TRP PREINCUBATED BEFORE PLATE SET-UP; DROP RATIO: 1:1
Crystal Properties Matthews coefficient Solvent content 3.3 62.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 138.91 α = 90 b = 138.91 β = 90 c = 142.59 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) 0.9164 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 2.33 50 100 0.13 0.998 14.09 20.84 66588
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 2.33 2.39 100 1.71 0.746 1.96 21.05
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-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 CHAINA 2.33 49.8 66549 3342 100 0.192 0.1956 0.237 0.2349 RANDOM 70.03
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] 0.337 0.168 0.337 -1.092
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.452 r_dihedral_angle_4_deg 18.463 r_dihedral_angle_3_deg 14.442 r_scangle_it 8.624 r_scangle_other 8.623 r_mcangle_it 8.313 r_mcangle_other 8.312 r_dihedral_angle_1_deg 7.251 r_scbond_it 6.163 r_scbond_other 6.162
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.452 r_dihedral_angle_4_deg 18.463 r_dihedral_angle_3_deg 14.442 r_scangle_it 8.624 r_scangle_other 8.623 r_mcangle_it 8.313 r_mcangle_other 8.312 r_dihedral_angle_1_deg 7.251 r_scbond_it 6.163 r_scbond_other 6.162 r_mcbond_it 6.085 r_mcbond_other 6.085 r_angle_refined_deg 1.476 r_angle_other_deg 1.253 r_nbd_refined 0.203 r_xyhbond_nbd_refined 0.18 r_nbtor_refined 0.166 r_nbd_other 0.16 r_chiral_restr 0.068 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbtor_other 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_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8401 Nucleic Acid Atoms Solvent Atoms 224 Heterogen Atoms 66
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing