6H44 | pdb_00006h44

Flavin-dependent Tryptophan 6-halogenase Thal in complex with tryptophan

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		Thal

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
2	VAPOR DIFFUSION, SITTING DROP	9	293	0.1 M bicine pH 9.0, 1.6 M K2HPO4/NaH2PO4 protein concentration: ~15 mg/mL protein buffer:10 mM Tris pH 7.4, 50 mM NaCl and 1 mM TCEP drop ratio: 1:1 (P:R)

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 136.7	α = 90
b = 136.7	β = 90
c = 144.9	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 6M-F		2017-05-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	0.9763	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	2.55	50	100	0.172	0.999	15.89	20.59		50056			52.5

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	2.55	2.62	100		1.776	0.666	2.07	20.74

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	THROUGHOUT	Thal	2.55	49.77	47558	2462	99.93	0.18118	0.17892	0.18	0.22506	0.23	RANDOM	56.068

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]
0.45	0.22		0.45		-1.46

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.638
r_dihedral_angle_4_deg	21.376
r_dihedral_angle_3_deg	15.009
r_long_range_B_refined	8.907
r_long_range_B_other	8.906
r_scangle_other	7.06
r_dihedral_angle_1_deg	6.791
r_mcangle_it	6.356
r_mcangle_other	6.355
r_scbond_it	4.81
r_scbond_other	4.81
r_mcbond_it	4.359
r_mcbond_other	4.359
r_angle_refined_deg	1.265
r_angle_other_deg	0.875
r_chiral_restr	0.061
r_bond_refined_d	0.008
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	8432
Nucleic Acid Atoms
Solvent Atoms	197
Heterogen Atoms	150

Software

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