7AQU

Flavin-dependent tryptophan halogenase Thal: N-terminally His-tagged form of quintuple mutant (NHis-Thal-RebH5)


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP9293.5reservoir solution: 0.1 M bicine pH 9.0, 20 % (w/v) PEG 4000, 10 % (v/v) glycerol, 0.02 M amino acid mix consisting of L-Glu, L-Ala, D-Ala, Gly, L-Lys, D-Lysis, L-Ser and D-Ser; protein buffer solution: 10 mM TRIS, 50 mM NaCl, 1 mM TCEP; protein concentration: ~15 mg/mL; drop ratio: 100 nL+100 nL (protein + reservoir)
Crystal Properties
Matthews coefficientSolvent content
2.346.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.58α = 90
b = 118.57β = 104.038
c = 87.1γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2018-06-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)0.9763PETRA 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
11.635096.60.0790.99915.337.0312908231.4
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)
11.631.6785.31.1460.7481.976.73

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE6H43 chain A1.6348.579129047647496.5640.1680.16670.202327.22
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]
1.086-0.784-0.9230.203
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.203
r_dihedral_angle_4_deg16.405
r_dihedral_angle_3_deg11.837
r_dihedral_angle_1_deg6.768
r_lrange_other6.339
r_lrange_it6.338
r_scangle_it4.581
r_scangle_other4.579
r_mcangle_other3.198
r_mcangle_it3.197
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.203
r_dihedral_angle_4_deg16.405
r_dihedral_angle_3_deg11.837
r_dihedral_angle_1_deg6.768
r_lrange_other6.339
r_lrange_it6.338
r_scangle_it4.581
r_scangle_other4.579
r_mcangle_other3.198
r_mcangle_it3.197
r_scbond_it3.056
r_scbond_other3.054
r_mcbond_it2.356
r_mcbond_other2.343
r_angle_refined_deg1.595
r_angle_other_deg1.457
r_symmetry_nbd_refined0.299
r_nbd_refined0.22
r_nbd_other0.196
r_symmetry_nbd_other0.179
r_nbtor_refined0.172
r_xyhbond_nbd_refined0.159
r_symmetry_xyhbond_nbd_refined0.134
r_chiral_restr0.084
r_ncsr_local_group_10.081
r_symmetry_nbtor_other0.079
r_symmetry_xyhbond_nbd_other0.055
r_bond_refined_d0.01
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8383
Nucleic Acid Atoms
Solvent Atoms975
Heterogen Atoms88

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing