6H43 | pdb_00006h43

Flavin-dependent Tryptophan 6-halogenase Thal

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2OAM	2OAM, 2AQJ, 2WEU, 5HY5
experimental model	PDB	2AQJ	2OAM, 2AQJ, 2WEU, 5HY5
experimental model	PDB	2WEU	2OAM, 2AQJ, 2WEU, 5HY5
experimental model	PDB	5HY5	2OAM, 2AQJ, 2WEU, 5HY5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	reservoir: 0.1 M Tris pH 8.5, 1.5 M K2HPO4/KH2PO4 protein concentration: ~ 15mg/mL drop ratio: 2:1 (P:R) protein buffer: 10 mM Tris pH 7.4, 50 mM NaCl and 1 mM TCEP

Crystal Properties
Matthews coefficient	Solvent content
3.25	62.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 139.47	α = 90
b = 139.47	β = 90
c = 142.51	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		2017-04-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	0.9	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	2.2	49.89	100	0.14	0.998	11.5	8.5		79654			52.9

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	2.2	2.26	100		1.841	0.634	2	8.4

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	2OAM, 2AQJ, 2WEU, 5HY5	2.2	49.89	75624	3990	99.97	0.17168	0.16966	0.18	0.2111	0.21	RANDOM	48.75

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]
0.53	0.26		0.53		-1.71

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.179
r_dihedral_angle_4_deg	19.72
r_dihedral_angle_3_deg	15.117
r_long_range_B_other	9.124
r_long_range_B_refined	9.121
r_scangle_other	7.403
r_dihedral_angle_1_deg	6.706
r_mcangle_it	5.714
r_mcangle_other	5.714
r_scbond_it	5.184
r_scbond_other	5.182
r_mcbond_other	4.118
r_mcbond_it	4.117
r_angle_refined_deg	1.457
r_angle_other_deg	0.931
r_chiral_restr	0.075
r_bond_refined_d	0.011
r_gen_planes_refined	0.007
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	8376
Nucleic Acid Atoms
Solvent Atoms	319
Heterogen Atoms	109

Software

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