8AD7

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6H436H43 CHAINA

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.2293RESERVOIR: 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 coefficientSolvent content
3.362.78

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 138.91α = 90
b = 138.91β = 90
c = 142.59γ = 120
Symmetry
Space GroupP 64

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2017-11-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)0.9164PETRA III, EMBL c/o DESYP13 (MX1)

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
12.33501000.130.99814.0920.8466588
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)
12.332.391001.710.7461.9621.05

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE6H43 CHAINA2.3349.86654933421000.1920.237RANDOM70.03
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]
0.3370.1680.337-1.092
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.452
r_dihedral_angle_4_deg18.463
r_dihedral_angle_3_deg14.442
r_scangle_it8.624
r_scangle_other8.623
r_mcangle_it8.313
r_mcangle_other8.312
r_dihedral_angle_1_deg7.251
r_scbond_it6.163
r_scbond_other6.162
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.452
r_dihedral_angle_4_deg18.463
r_dihedral_angle_3_deg14.442
r_scangle_it8.624
r_scangle_other8.623
r_mcangle_it8.313
r_mcangle_other8.312
r_dihedral_angle_1_deg7.251
r_scbond_it6.163
r_scbond_other6.162
r_mcbond_it6.085
r_mcbond_other6.085
r_angle_refined_deg1.476
r_angle_other_deg1.253
r_nbd_refined0.203
r_xyhbond_nbd_refined0.18
r_nbtor_refined0.166
r_nbd_other0.16
r_chiral_restr0.068
r_bond_refined_d0.007
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
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 AtomsNumber
Protein Atoms8401
Nucleic Acid Atoms
Solvent Atoms224
Heterogen Atoms66

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing