8AD8

Flavin-dependent tryptophan 6-halogenase Thal in complex with a D-Trp-Ser dipeptide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6H43 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP9293Reservoir 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 coefficientSolvent content
3.2562.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 137.2α = 90
b = 137.2β = 90
c = 143.8γ = 120
Symmetry
Space GroupP 64

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2020-03-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.20.9184BESSY14.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim I (All)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.9547.981000.1540.99816.7110.543239669
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.953.031001.540.6761.9911.03

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE6H432.9547.9830787157799.920.195280.192440.24988RANDOM70.78
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]
1.230.621.23-4
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.401
r_dihedral_angle_4_deg17.188
r_dihedral_angle_3_deg16.326
r_long_range_B_refined11.792
r_long_range_B_other11.792
r_mcangle_it9.106
r_mcangle_other9.104
r_scangle_other8.95
r_dihedral_angle_1_deg7.5
r_mcbond_it6.137
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.401
r_dihedral_angle_4_deg17.188
r_dihedral_angle_3_deg16.326
r_long_range_B_refined11.792
r_long_range_B_other11.792
r_mcangle_it9.106
r_mcangle_other9.104
r_scangle_other8.95
r_dihedral_angle_1_deg7.5
r_mcbond_it6.137
r_mcbond_other6.135
r_scbond_it5.947
r_scbond_other5.94
r_angle_refined_deg1.465
r_angle_other_deg1.217
r_chiral_restr0.064
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
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 AtomsNumber
Protein Atoms8297
Nucleic Acid Atoms
Solvent Atoms6
Heterogen Atoms38

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing