8AD8 | pdb_00008ad8

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6H43

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	9	293	Reservoir 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 coefficient	Solvent content
3.25	62.16

Crystal Data

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

Symmetry
Space Group	P 64

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 2M		2020-03-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.2	0.9184	BESSY	14.2

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	2.95	47.98	100	0.154	0.998	16.71	10.54		32396			69

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	2.95	3.03	100		1.54	0.676	1.99	11.03

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	FREE R-VALUE	6H43	2.95	47.98	30787	1577	99.92	0.19528	0.19244	0.19	0.24988	0.25	RANDOM	70.78

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]
1.23	0.62		1.23		-4

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.401
r_dihedral_angle_4_deg	17.188
r_dihedral_angle_3_deg	16.326
r_long_range_B_refined	11.792
r_long_range_B_other	11.792
r_mcangle_it	9.106
r_mcangle_other	9.104
r_scangle_other	8.95
r_dihedral_angle_1_deg	7.5
r_mcbond_it	6.137
r_mcbond_other	6.135
r_scbond_it	5.947
r_scbond_other	5.94
r_angle_refined_deg	1.465
r_angle_other_deg	1.217
r_chiral_restr	0.064
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
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	8297
Nucleic Acid Atoms
Solvent Atoms	6
Heterogen Atoms	38

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing